Therapeutic compounds and uses thereof

ABSTRACT

Described herein are compounds of Formula (I) or Formula (VI), pharmaceutically acceptable salts thereof, and pharmaceutical compositions thereof. Also provided are particles (e.g., nanoparticles) comprising compounds of Formula (I) or Formula (VI) and pharmaceutical compositions thereof that are mucus penetrating. Methods of using the compounds or pharmaceutical compositions thereof for treating diseases are also provided.

FIELD OF THE INVENTION

This invention relates to therapeutic compounds and methods of treatingproliferative diseases and diseases associated with anagiogenesis suchas cancer and macular degeneration.

BACKGROUND OF THE INVENTION

Growth factors play an important role in angiogenesis,lymphangiogenesis, and vasculogenesis. Growth factors regulateangiogenesis in a variety of processes including embryonic development,wound healing, and several aspects of female reproductive function.Undesirable or pathological angiogenesis is associated with diseasesincluding diabetic retinopathy, psoriasis, cancer, rheumatoid arthritis,atheroma, Kaposi's sarcoma, and hemangioma (Fan et al., 1995, TrendsPharmacol. Sci. 16: 57 66; Folkman, 1995, Nature Medicine 1: 27 31).Angiogenic ocular conditions represent the leading cause of irreversiblevision loss in developed countries. In the United States, for example,retinopathy of prematurity, diabetic retinopathy, and age-relatedmacular degeneration are the principal causes of blindness in infants,working age adults, and the elderly, respectively. Efforts have beendeveloped to promote angiogenesis in treatment of these conditions (R.Roskoski Jr., Critical Reviews in Oncology/Hematology, 62 (2007),179-213).

Therefore, there is a need for new therapeutic compounds for thetreatment of diseases associated with aberrant signaling of growthfactors, such as cancer, macular degeneration, and diabetic retinopathy.

SUMMARY OF THE INVENTION

The present invention provides compounds of Formulae (I)-(VI),pharmaceutical compositions thereof, and kits to treat proliferativediseases, ocular diseases, dermatological diseases, inflammationdiseases, or metabolic diseases. The present invention also providesmethods of using the inventive compounds, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, or prodrugsthereof, and compositions thereof, to study the inhibition of growthfactor signaling and/or to treat and/or prevent proliferative diseases,ocular diseases, dermatological diseases, inflammation diseases, ormetabolic diseases. The inventive compounds are particularly useful intreating diseases associated with angiogenesis.

In one aspect, the present invention provides compounds of Formula (I):

and pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,Z, m, and n are as defined herein.

In one aspect, the present invention provides compounds of Formula (II):

and pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, R₄,X, Y, m, n, and j are as defined herein.

In one aspect, the present invention provides compounds of Formula(III):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, R₅, X,Y, m, n, and k are as defined herein.

In one aspect, the present invention provides compounds of Formula (IV):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,Z₁, m, and n are as defined herein.

In one aspect, the present invention provides compounds of Formula (V):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,e, f, m, and n are as defined herein.

In one aspect, the present invention provides compounds of Formula (VI):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,Z, m, and n are as defined herein.

In another aspect, the present invention provides pharmaceuticalcompositions including a compound of Formula (I), or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, andoptionally a pharmaceutically acceptable carrier. In certainembodiments, the pharmaceutical compositions described herein include atherapeutically effective amount of a compound of Formula (I), or apharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof. The pharmaceutical composition may be useful fortreating proliferative diseases, ocular diseases, dermatologicaldiseases, inflammation diseases, and metabolic diseases. In certainembodiments, the ocular disease being treated is macular degeneration.

In another aspect, the present invention provides pharmaceuticalcompositions including a compound of Formula (VI), or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, andoptionally a pharmaceutically acceptable carrier. In certainembodiments, the pharmaceutical compositions described herein include atherapeutically effective amount of a compound of Formula (VI), or apharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof. The pharmaceutical composition may be useful fortreating proliferative diseases, ocular diseases, dermatologicaldiseases, inflammation diseases, and metabolic diseases. In certainembodiments, the ocular disease being treated is macular degeneration.

In some embodiments, the compounds described herein may be intended fordelivery in a subject's tissues having mucus (e.g., eye, respiratorytract, gastrointestinal tract, genito-urinary tract), which is aviscoelastic and adhesive substance that traps most foreign objects(e.g., microorganisms, particles, dust). For effective drug delivery,compound or particles that are immobilized in the mucus are quicklyeliminated by mucus clearance mechanisms; therefore, they are not ableto effectively deliver the intended therapeutic effect. In thesetissues, for the compound to effective, it must quickly penetrate themucus and/or avoid mucus clearance mechanisms. Accordingly, modifyingmucoadhesive compounds or particles containing compounds with a coatingto reduce the mucoadhesiveness, and decreasing the size of the particlesof compound may allow for efficient delivery and therapeutic effect.

In one aspect of the invention, the compounds described herein areformulated into mucus penetrating particles or mucus penetratingcrystals (collectively, MPPs) suitable for administration (e.g., topicalor inhalation) to tissues of the subject having mucus (e.g., eye,respiratory tract, gastrointestinal tract, genito-urinary tract). Incertain embodiments, the inventive compounds are crystalline.

In another aspect, the present invention provides particles containing acompound described herein or particles comprising a compound describedherein. In certain embodiments, the particles are mucus penetrating. Theparticles of the invention may include a coating surrounding a core. Thecore may contain primarily a compound of the invention, or the core maybe a polymeric core with the compound encapsulated in the polymer. Incertain embodiments, the inventive particles are nanoparticles (e.g.,particles having an average diameter of at least about 10 nm and lessthan about 1 μm). The inventive particles may be useful in deliveringthe pharmaceutical agent to a subject. In certain embodiments, theparticles of the invention are capable of delivering the pharmaceuticalagent in or through mucus of a subject.

Another aspect of the invention relates to pharmaceutical compositionscomprising an inventive compound and/or a plurality of inventiveparticles. In certain embodiments, the pharmaceutical compositions areuseful in delivering a pharmaceutical agent (e.g., the compound of theinvention) to a subject.

In another aspect of the invention, the present invention providespharmaceutical composition comprising a plurality of particlescomprising (i) a core comprising a compound of the invention describedherein, or a pharmaceutically acceptable salt thereof, and (ii) acoating of a surface altering agent surrounding the core, wherein thesurface altering agent is present on the outer surface of the core at adensity of at least 0.01 surface altering agent per nm², and optionally,at least one pharmaceutically acceptable excipient. In some embodiments,the surface altering agent is a triblock copolymer of the structure(hydrophilic block)-(hydrophobic block)-(hydrophilic block). In someaspects, the triblock copolymer is a PLURONIC or poloxamer.

In certain embodiments, the compound, particle, or pharmaceuticalcomposition is formulated to be mucus penetrating.

In another aspect, the present invention provides methods of treating orpreventing a disease by administering to a subject in need thereof atherapeutically effective amount of a compound of Formula (I). Thediseases include proliferative diseases, ocular diseases (e.g., maculardegeneration), dermatological diseases, inflammation diseases, andmetabolic diseases.

In another aspect, the present invention provides methods of treating orpreventing a disease by administering to a subject in need thereof atherapeutically effective amount of a compound of Formula (VI). Thediseases include proliferative diseases, ocular diseases (e.g., maculardegeneration), dermatological diseases, inflammation diseases, andmetabolic diseases.

In another aspect, the present invention provides kits comprising acompound of Formula (I) or (VI), or a pharmaceutically acceptable salt,solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer,isotopically labeled derivative, or prodrug thereof, or a pharmaceuticalcomposition thereof. The kits of the invention may include a single doseor multiple doses of a compound of Formula (I), or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, or apharmaceutical composition thereof. The provided kits may be useful forthe treatment of proliferative diseases, ocular diseases, dermatologicaldiseases, inflammation diseases, or metabolic diseases. In certainembodiments, the kits described herein further include instructions foradministering the compound of Formula (I) or (VI), or thepharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, or the pharmaceutical composition thereof. The kits mayalso include packaging information describing the use or prescribinginformation for the subject or a health care professional. Suchinformation may be required by a regulatory agency such as the U.S. Foodand Drug Administration (FDA). The kit may also optionally include adevice for administration of the compound or composition, for example, adropper for ocular administration or a syringe for parenteraladministration.

The details of certain embodiments of the invention are set forthherein. Other features, objects, and advantages of the invention will beapparent from the Detailed Description, Figures, Examples, and Claims.

DEFINITIONS Chemical Definitions

Definitions of specific functional groups and chemical terms aredescribed in more detail below. The chemical elements are identified inaccordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, andspecific functional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in ThomasSorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition,John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive OrganicTransformations, VCH Publishers, Inc., New York, 1989; and Carruthers,Some Modern Methods of Organic Synthesis, 3^(rd) Edition, CambridgeUniversity Press, Cambridge, 1987.

Compounds described herein can comprise one or more asymmetric centers,and thus can exist in various isomeric forms, e.g., enantiomers and/ordiastereomers. For example, the compounds described herein can be in theform of an individual enantiomer, diastereomer or geometric isomer, orcan be in the form of a mixture of stereoisomers, including racemicmixtures and mixtures enriched in one or more stereoisomer. Isomers canbe isolated from mixtures by methods known to those skilled in the art,including chiral high pressure liquid chromatography (HPLC) and theformation and crystallization of chiral salts; or preferred isomers canbe prepared by asymmetric syntheses. See, for example, Jacques et al.,Enantiomers, Racemates and Resolutions (Wiley Interscience, New York,1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistryof Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, Tables ofResolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ.of Notre Dame Press, Notre Dame, Ind. 1972). The invention additionallyencompasses compounds described herein as individual isomerssubstantially free of other isomers, and alternatively, as mixtures ofvarious isomers.

When a range of values is listed, it is intended to encompass each valueand sub-range within the range. For example “C₁₋₆” is intended toencompass C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆,C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆.

As used herein, a “hydrocarbon chain” refers to a substituted orunsubstituted divalent alkyl, alkenyl, or alkynyl group. A hydrocarbonchain includes at least one chain, each node (“carbon unit”) of whichincluding at least one carbon atom between the two radicals of thehydrocarbon chain. For example, hydrocarbon chain—C^(A)H(C^(B)H₂C^(C)H₃)— includes only one carbon unit C^(A). The term“C_(X) hydrocarbon chain,” wherein x is a positive integer, refers to ahydrocarbon chain that includes x number of carbon unit(s) between thetwo radicals of the hydrocarbon chain. If there is more than onepossible value of x, the smallest possible value of x is used for thedefinition of the hydrocarbon chain. For example, —CH(C₂H₅)— is a C₁hydrocarbon chain, and

is a C₃ hydrocarbon chain. When a range of values is used, e.g., a C₁₋₆hydrocarbon chain, the meaning of the range is as described herein. Ahydrocarbon chain may be saturated (e.g., —(CH₂)₄—). A hydrocarbon chainmay also be unsaturated and include one or more C═C and/or C≡C bondsanywhere in the hydrocarbon chain. For instance, —CH═CH—(CH₂)₂—,—CH₂—C≡C—CH₂—, and —C≡C—CH═CH— are all examples of a unsubstituted andunsaturated hydrocarbon chain. In certain embodiments, the hydrocarbonchain is unsubstituted (e.g., —(CH₂)₄—). In certain embodiments, thehydrocarbon chain is substituted (e.g., —CH(C₂H₅)— and —CF₂—). Any twosubstituents on the hydrocarbon chain may be joined to form anoptionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, or optionally substituted heteroaryl ring.For instance,

are all examples of a hydrocarbon chain. In contrast, in certainembodiments

are not within the scope of the hydrocarbon chains described herein.

“Alkyl” refers to a radical of a straight-chain or branched saturatedhydrocarbon group having from 1 to 20 carbon atoms (“C₁₋₂₀ alkyl”). Insome embodiments, an alkyl group has 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), n-propyl(C₃), isopropyl (C₃), n-butyl (C₄), tert-butyl (C₄), sec-butyl (C₄),iso-butyl (C₄), n-pentyl (C₅), 3-pentanyl (C₅), amyl (C₅), neopentyl(C₅), 3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n-hexyl (C₆).Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈),and the like. Unless otherwise specified, each instance of an alkylgroup is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkyl”) or substituted (a “substituted alkyl”) with oneor more substituents. In certain embodiments, the alkyl group isunsubstituted C₁₋₁₀ alkyl (e.g., —CH₃). In certain embodiments, thealkyl group is substituted C₁₋₁₀ alkyl.

“Alkenyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon double bonds, and no triple bonds (“C₂₋₂₀ alkenyl”). Insome embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms(“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenylgroup has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, analkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In someembodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”).In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂alkenyl”). The one or more carbon-carbon double bonds can be internal(such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples ofC₂₋₄ alkenyl groups include ethenyl (C₂), 1 -propenyl (C₃), 2-propenyl(C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like.Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenylgroups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and thelike. Additional examples of alkenyl include heptenyl (C₇), octenyl(C₈), octatrienyl (C₈), and the like. Unless otherwise specified, eachinstance of an alkenyl group is independently optionally substituted,i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certainembodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. Incertain embodiments, the alkenyl group is substituted C₂₋₁₀alkenyl.

“Alkynyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon triple bonds, and optionally one or more double bonds(“C₂₋₂₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 10carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl grouphas 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, analkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In someembodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”).In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms(“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynylgroup has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbontriple bonds can be internal (such as in 2-butynyl) or terminal (such asin 1-butynyl). Examples of C₂₋₄ alkynyl groups include, withoutlimitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl(C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₆ alkenyl groupsinclude the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅),hexynyl (C₆), and the like. Additional examples of alkynyl includeheptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified,each instance of an alkynyl group is independently optionallysubstituted, i.e., unsubstituted (an “unsubstituted alkynyl”) orsubstituted (a “substituted alkynyl”) with one or more substituents. Incertain embodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl.In certain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

“Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromaticcyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. Insome embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms(“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, acarbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). Insome embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms(“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include,without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl(C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅),cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like.Exemplary C₃₋₈ carbocyclyl groups include, without limitation, theaforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇),cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇),cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇),bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclylgroups include, without limitation, the aforementioned C₃₋₈ carbocyclylgroups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀),cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl(C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examplesillustrate, in certain embodiments, the carbocyclyl group is eithermonocyclic (“monocyclic carbocyclyl”) or contains a fused, bridged, orspiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) andcan be saturated or partially unsaturated. “Carbocyclyl” also includesring systems wherein the carbocyclic ring, as defined above, is fused toone or more aryl or heteroaryl groups wherein the point of attachment ison the carbocyclic ring, and in such instances, the number of carbonscontinue to designate the number of carbons in the carbocyclic ringsystem. Unless otherwise specified, each instance of a carbocyclyl groupis independently optionally substituted, i.e., unsubstituted (an“unsubstituted carbocyclyl”) or substituted (a “substitutedcarbocyclyl”) with one or more substituents. In certain embodiments, thecarbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl. In certainembodiments, the carbocyclyl group is a substituted C₃₋₁₀ carbocyclyl.In some embodiments, “carbocyclyl” is a monocyclic, saturatedcarbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ringcarbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkylgroup has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In someembodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ringcarbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groupsinclude cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups aswell as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups aswell as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwisespecified, each instance of a cycloalkyl group is independentlyunsubstituted (an “unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certainembodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. Incertain embodiments, the cycloalkyl group is substituted C₃₋₁₀cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to10-membered non-aromatic ring system having ring carbon atoms and 1 to 4ring heteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 memberedheterocyclyl”). In certain embodiments, the heteroatom is independentlyselected from nitrogen, sulfur, and oxygen. In heterocyclyl groups thatcontain one or more nitrogen atoms, the point of attachment can be acarbon or nitrogen atom, as valency permits. A heterocyclyl group caneither be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged orspiro ring system such as a bicyclic system (“bicyclic heterocyclyl”),and can be saturated or partially unsaturated. Heterocyclyl bicyclicring systems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring,as defined above, is fused with one or more carbocyclyl groups whereinthe point of attachment is either on the carbocyclyl or heterocyclicring, or ring systems wherein the heterocyclic ring, as defined above,is fused with one or more aryl or heteroaryl groups, wherein the pointof attachment is on the heterocyclic ring, and in such instances, thenumber of ring members continue to designate the number of ring membersin the heterocyclic ring system. Unless otherwise specified, eachinstance of heterocyclyl is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certainembodiments, the heterocyclyl group is unsubstituted 3-10 memberedheterocyclyl. In certain embodiments, the heterocyclyl group issubstituted 3-10 membered heterocyclyl. In some embodiments, aheterocyclyl group is a 5-10 membered non-aromatic ring system havingring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom isindependently selected from nitrogen, oxygen, sulfur, boron, phosphorus,and silicon (“5-10 membered heterocyclyl”). In some embodiments, aheterocyclyl group is a 5-8 membered non-aromatic ring system havingring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom isindependently selected from nitrogen, oxygen, and sulfur (“5-8 memberedheterocyclyl”). In some embodiments, a heterocyclyl group is a 5-6membered non-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”). In someembodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclylhas one ring heteroatom selected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing one heteroatominclude, without limitation, azirdinyl, oxiranyl, and thiorenyl.Exemplary 4-membered heterocyclyl groups containing one heteroatominclude, without limitation, azetidinyl, oxetanyl, and thietanyl.Exemplary 5-membered heterocyclyl groups containing one heteroatominclude, without limitation, tetrahydrofuranyl, dihydrofuranyl,tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl,and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groupscontaining two heteroatoms include, without limitation, dioxolanyl,oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-memberedheterocyclyl groups containing three heteroatoms include, withoutlimitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary6-membered heterocyclyl groups containing one heteroatom include,without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl,and thianyl. Exemplary 6-membered heterocyclyl groups containing twoheteroatoms include, without limitation, piperazinyl, morpholinyl,dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groupscontaining two heteroatoms include, without limitation, triazinanyl.Exemplary 7-membered heterocyclyl groups containing one heteroatominclude, without limitation, azepanyl, oxepanyl, and thiepanyl.Exemplary 8-membered heterocyclyl groups containing one heteroatominclude, without limitation, azocanyl, oxecanyl, and thiocanyl.Exemplary 5-membered heterocyclyl groups fused to a C₆ aryl ring (alsoreferred to herein as a 5,6-bicyclic heterocyclic ring) include, withoutlimitation, indolinyl, isoindolinyl, dihydrobenzofuranyl,dihydrobenzothienyl, benzoxazolinonyl, and the like. Exemplary6-membered heterocyclyl groups fused to an aryl ring (also referred toherein as a 6,6-bicyclic heterocyclic ring) include, without limitation,tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclicor tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 πelectrons shared in a cyclic array) having 6-14 ring carbon atoms andzero heteroatoms in the aromatic ring system (“C₆₋₁₄ aryl”). In someembodiments, an aryl group has six ring carbon atoms (“C₆ aryl”; e.g.,phenyl). In some embodiments, an aryl group has ten ring carbon atoms(“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In someembodiments, an aryl group has fourteen ring carbon atoms (“C₁₋₄ aryl”;e.g., anthracyl). “Aryl” also includes ring systems wherein the arylring, as defined above, is fused with one or more carbocyclyl orheterocyclyl groups wherein the radical or point of attachment is on thearyl ring, and in such instances, the number of carbon atoms continue todesignate the number of carbon atoms in the aryl ring system. Unlessotherwise specified, each instance of an aryl group is independentlyoptionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) orsubstituted (a “substituted aryl”) with one or more substituents. Incertain embodiments, the aryl group is unsubstituted C₆₋₁₄ aryl. Incertain embodiments, the aryl group is substituted C₆₋₁₄ aryl.

“Arylalkyl” is a subset of alkyl and aryl, as defined herein, and refersto an optionally substituted alkyl group substituted by an optionallysubstituted aryl group. In certain embodiments, the aralkyl isoptionally substituted benzyl. In certain embodiments, the aralkyl isbenzyl. In certain embodiments, the aralkyl is optionally substitutedphenethyl. In certain embodiments, the aralkyl is phenethyl.

“Heteroaryl” refers to a radical of a 5-10 membered monocyclic orbicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 π electronsshared in a cyclic array) having ring carbon atoms and 1-4 ringheteroatoms provided in the aromatic ring system, wherein eachheteroatom is independently selected from nitrogen, oxygen, and sulfur(“5-10 membered heteroaryl”). In heteroaryl groups that contain one ormore nitrogen atoms, the point of attachment can be a carbon or nitrogenatom, as valency permits. Heteroaryl bicyclic ring systems can includeone or more heteroatoms in one or both rings. “Heteroaryl” includes ringsystems wherein the heteroaryl ring, as defined above, is fused with oneor more carbocyclyl or heterocyclyl groups wherein the point ofattachment is on the heteroaryl ring, and in such instances, the numberof ring members continue to designate the number of ring members in theheteroaryl ring system. “Heteroaryl” also includes ring systems whereinthe heteroaryl ring, as defined above, is fused with one or more arylgroups wherein the point of attachment is either on the aryl orheteroaryl ring, and in such instances, the number of ring membersdesignates the number of ring members in the fused (aryl/heteroaryl)ring system. Bicyclic heteroaryl groups wherein one ring does notcontain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and thelike) the point of attachment can be on either ring, i.e., either thering bearing a heteroatom (e.g., 2-indolyl) or the ring that does notcontain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”)with one or more substituents. In certain embodiments, the heteroarylgroup is unsubstituted 5-14 membered heteroaryl. In certain embodiments,the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatominclude, without limitation, pyrrolyl, furanyl, and thiophenyl.Exemplary 5-membered heteroaryl groups containing two heteroatomsinclude, without limitation, imidazolyl, pyrazolyl, oxazolyl,isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroarylgroups containing three heteroatoms include, without limitation,triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-memberedheteroaryl groups containing four heteroatoms include, withoutlimitation, tetrazolyl. Exemplary 6-membered heteroaryl groupscontaining one heteroatom include, without limitation, pyridinyl.Exemplary 6-membered heteroaryl groups containing two heteroatomsinclude, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.Exemplary 6-membered heteroaryl groups containing three or fourheteroatoms include, without limitation, triazinyl and tetrazinyl,respectively. Exemplary 7-membered heteroaryl groups containing oneheteroatom include, without limitation, azepinyl, oxepinyl, andthiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, withoutlimitation, indolyl, isoindolyl, indazolyl, benzotriazolyl,benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl,benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl,benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, andpurinyl. Exemplary 6,6-bicyclic heteroaryl groups include, withoutlimitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.

“Heteroaralkyl” is a subset of alkyl and heteroaryl, as defined herein,and refers to an optionally substituted alkyl group substituted by anoptionally substituted heteroaryl group.

“Partially unsaturated” refers to a group that includes at least onedouble or triple bond. A “partially unsaturated” ring system is furtherintended to encompass rings having multiple sites of unsaturation but isnot intended to include aromatic groups (e.g., aryl or heteroarylgroups) as herein defined. Likewise, “saturated” refers to a group thatdoes not contain a double or triple bond, i.e., contains all singlebonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, as defined herein, which are divalent bridging groups arefurther referred to using the suffix -ene, e.g., alkylene, alkenylene,alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.

As used herein, the term “optionally substituted” refers to asubstituted or unsubstituted moiety.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, as defined herein, are optionally substituted (e.g.,“substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted”alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or“unsubstituted” carbocyclyl, “substituted” or “unsubstituted”heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or“unsubstituted” heteroaryl group). In general, the term “substituted”,whether preceded by the term “optionally” or not, means that at leastone hydrogen present on a group (e.g., a carbon or nitrogen atom) isreplaced with a permissible substituent, e.g., a substituent which uponsubstitution results in a stable compound, e.g., a compound which doesnot spontaneously undergo transformation such as by rearrangement,cyclization, elimination, or other reaction. Unless otherwise indicated,a “substituted” group has a substituent at one or more substitutablepositions of the group, and when more than one position in any givenstructure is substituted, the substituent is either the same ordifferent at each position. The term “substituted” is contemplated toinclude substitution with all permissible substituents of organiccompounds, any of the substituents described herein that results in theformation of a stable compound. The present invention contemplates anyand all such combinations in order to arrive at a stable compound. Forpurposes of this invention, heteroatoms such as nitrogen may havehydrogen substituents and/or any suitable substituent as describedherein which satisfy the valencies of the heteroatoms and results in theformation of a stable moiety.

Exemplary carbon atom substituents include, but are not limited to,halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂,N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa),—SSR_(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂,—NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂,—NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa),—S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃,—OSi(R^(aa))₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa),—SC(═S)SR^(aa), —SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa),—SC(═O)R^(aa), —P(═O)₂R^(aa), —OP(═O)₂R^(aa), —P(═O)(R^(aa))₂,—OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂,—OP(═O)₂N(R^(bb))₂, —P(═O)(NR^(bb))₂, —OP(═O)(NR^(bb))₂,—NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(NR^(bb))₂, —P(R^(cc))₂,—P(R^(cc))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —B(R^(aa))₂, —B(OR^(cc))₂,—BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

or two geminal hydrogens on a carbon atom are replaced with the group═O, ═S, ═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa),═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(aa) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH,—OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂,—SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc),—C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂,—P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, or two R^(bb) groups are joined to form a 3-14membered heterocyclyl or 5-14 membered heteroaryl ring, wherein eachalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylis independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN,—NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee), —ON(R^(ff))₂, —N(R^(ff))₂,—N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff), —SH, —SR^(ee), —SSR^(ee),—C(═O)R^(ee), —CO₂H, —CO₂R^(ee), —OC(═O)R^(ee), —OCO₂R^(ee),—C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NR^(ff)C(═O)R^(ee),—NR^(ff)CO₂R^(ee), —NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(ee),—OC(═NR^(ff))R^(ee), —OC(═NR^(ff))OR^(ee), —C(═NR^(ff))N(R^(ff))₂,—OC(═NR^(ff))N(R^(ff))₂, —NR^(ff)C(═NR^(ff))N(R^(ff))₂,—NR^(ff)SO₂R^(ee), —SO₂N(R^(ff))₂, —SO₂R^(ee), —SO₂OR^(ee), —OSO₂R^(ee),—S(═O)R^(ee), —Si(R^(ee))₃, —OSi(R^(ee))₃, —C(═S)N(R^(ff))₂,—C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O)₂R^(ee),—P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10membered heterocyclyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups, or two geminal R^(dd) substituents can be joined to form ═O or═S;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl,C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, ortwo R^(ff) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

-   -   each instance of R^(gg) is, independently, halogen, —CN, —NO₂,        —N₃, —SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆        alkyl)₂, —N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆        alkyl)⁺X⁻, —NH₃ ⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆        alkyl), —NH(OH), —SH, —SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆        alkyl), —CO₂H, —CO₂(C₁₋₆ alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆        alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆ alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl),        —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆ alkyl)C(═O)(C₁₋₆ alkyl),        —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂, —NHC(═O)NH(C₁₋₆        alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆ alkyl),        —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆        alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆        alkyl), —OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂,        —NHSO₂(C₁₋₆ alkyl), —SO₂N(C₁₋₆ alkyl)₂, —SO₂NH(C₁₋₆ alkyl),        —SO₂NH₂, —SO₂C₁₋₆ alkyl, —SO₂OC₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl,        —SOC₁₋₆ alkyl, —Si(C₁₋₆ alkyl)₃, —OSi(C₁₋₆ alkyl)₃-C(═S)N(C₁₋₆        alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂, —C(═O)S(C₁₋₆ alkyl),        —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆ alkyl),        —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆        alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆        alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered        heterocyclyl, 5-10 membered heteroaryl; or two geminal R^(gg)        substituents can be joined to form ═O or ═S; wherein X⁻ is a        counterion.

A “counterion” or “anionic counterion” is a negatively charged groupassociated with a cationic quaternary amino group in order to maintainelectrostatic neutrality. Exemplary counterions include halide ions(e.g., F⁻, Cl⁻, Br⁻, I⁻), NO₃ ⁻, ClO₄ ⁻, OH⁻, H₂PO₄ ⁻, HSO₄ ⁻, sulfonateions (e.g., methansulfonate, trifluoromethanesulfonate,p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate,naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate,ethan-1-sulfonic acid-2-sulfonate, and the like), and carboxylate ions(e.g., acetate, ethanoate, propanoate, benzoate, glycerate, lactate,tartrate, glycolate, and the like).

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro,—Cl), bromine (bromo, —Br), or iodine (iodo, —I).

“Acyl” as used herein refers to a moiety selected from the groupconsisting of —C(═O)R^(aa), CHO, —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—C(═O)NR^(bb)SO₂R^(aa), —C(═S)N(R^(bb))₂, —C(═O)SR^(aa), and—C(═S)SR^(aa), wherein R^(aa) and R^(bb) are as defined herein.

Nitrogen atoms can be substituted or unsubstituted as valency permits,and include primary, secondary, tertiary, and quarternary nitrogenatoms. Exemplary nitrogen atom substituents include, but are not limitedto, hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa),—C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa),—C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc),—SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc),—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂,C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups attached to a nitrogen atom are joinedto form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring,wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl,and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 ,R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc), and R^(dd) are asdefined above.

In certain embodiments, the substituent present on a nitrogen atom is anitrogen protecting group (also referred to as an amino protectinggroup). Nitrogen protecting groups include, but are not limited to, —OH,—OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa),—C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc),—SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl(e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aralkyl, aryl, and heteroaryl is independently substitutedwith 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb),R^(cc) and R^(dd) are as defined herein. Nitrogen protecting groups arewell known in the art and include those described in Protecting Groupsin Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition,John Wiley & Sons, 1999, incorporated herein by reference.

For example, nitrogen protecting groups such as amide groups (e.g.,—C(═O)R^(aa)) include, but are not limited to, formamide, acetamide,chloroacetamide, trichloroacetamide, trifluoroacetamide,phenylacetamide, 3-phenylpropanamide, picolinamide,3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide,p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide,acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide,3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,2-methyl-2-(o-nitrophenoxy)propanamide,2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethioninederivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g.,—C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethylcarbamante, 9-fluorenylmethyl carbamate (Fmoc),9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethylcarbamate,2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methylcarbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate(Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethylcarbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate,1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC),1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC),1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethylcarbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinylcarbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate(Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc),8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithiocarbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzylcarbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate,2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate,2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methylcarbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc),2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate(Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc),1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate,p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate,2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenylcarbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate,3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methylcarbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzylcarbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentylcarbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate,2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzylcarbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate,isobutyl carbamate, isonicotinyl carbamate,p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate,1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate,1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate,p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate,4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzylcarbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g.,—S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide(Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide(Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb),2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide(Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide(Ms), f3-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide,4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to,phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacylderivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanylderivative, N-acetylmethionine derivative,4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts),N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole,N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE),5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine,N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammoniumsalts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),N-9-phenylfluorenylamine (PhF),N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm),N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine,N-benzylideneamine, N-p-methoxybenzylideneamine,N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine,N-p-nitrobenzylideneamine, N-salicylideneamine,N-5-chlorosalicylideneamine,N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine,N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,N-borane derivative, N-diphenylborinic acid derivative,N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate,N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide,diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt),diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzylphosphoramidate, diphenyl phosphoramidate, benzenesulfenamide,o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide,pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).

In certain embodiments, the substituent present on an oxygen atom is anoxygen protecting group (also referred to as a hydroxyl protectinggroup). Oxygen protecting groups include, but are not limited to,—R^(aa), —N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa),—C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa),—C(═NR^(bb))N(R^(bb))₂, —S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃,—P(R^(cc))₂, —P(R^(cc))₃, —P(═O)₂R^(aa), —P(═O)(R^(aa))₂,—P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and —P(═O)(NR^(bb))₂, whereinR^(aa), R^(bb), and R^(cc) are as defined herein. Oxygen protectinggroups are well known in the art and include those described inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

Exemplary oxygen protecting groups include, but are not limited to,methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl,(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM),p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM),guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM),siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl,bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR),tetrahydropyranyl (THP), 3-bromotetrahydropyranyl,tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl(MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranylS,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl(CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl,t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl,benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl,p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl,p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido,diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl,triphenylmethyl, α-naphthyldiphenylmethyl,p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl,tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl,4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl,4,4′,4″-tris(levulinoyloxyphenyl)methyl,4,4′,4″-tris(benzoyloxyphenyl)methyl,3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl,1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl,9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl(TMS), triethylsilyl (TES), triisopropylsilyl (TIPS),dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS),dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl(TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate,benzoylformate, acetate, chloroacetate, dichloroacetate,trichloroacetate, trifluoroacetate, methoxyacetate,triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate,3-phenylpropionate, 4-oxopentanoate (levulinate),4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate,adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate,2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate(TMSEC), 2-(phenylsulfonyl)ethyl carbonate (Psec),2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutylcarbonate, alkyl vinyl carbonate alkyl allyl carbonate, t-butylcarbonate (BOC), alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate,alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate,alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkylS-benzyl thiocarbonate, 4-ethoxy-1-napththyl carbonate, methyldithiocarbonate, 2-iodobenzoate, 4-azidobutyrate,4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,2,6-dichloro-4-methylphenoxyacetate,2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate,o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkylN,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate(Ts).

In certain embodiments, the substituent present on a sulfur atom is asulfur protecting group (also referred to as a thiol protecting group).Sulfur protecting groups include, but are not limited to, —R^(aa),—N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃,—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and—P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein. Sulfur protecting groups are well known in the art and includethose described in Protecting Groups in Organic Synthesis, T. W. Greeneand P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporatedherein by reference.

These and other exemplary substituents are described in more detail inthe Detailed Description, Figures, Examples, and Claims. The inventionis not intended to be limited in any manner by the above exemplarylisting of substituents.

Other Definitions

The following definitions are more general terms used throughout thepresent application.

As used herein, the term “pharmaceutically acceptable salt” refers tothose salts which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswithout undue toxicity, irritation, allergic response and the like, andare commensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, Berge et al.,describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein byreference. Pharmaceutically acceptable salts of the compounds of thisinvention include those derived from suitable inorganic and organicacids and bases. Examples of pharmaceutically acceptable, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid, and perchloric acid or with organic acids such as acetic acid,oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, ormalonic acid or by using other methods known in the art such as ionexchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium and N⁺(C₁₋₄ alkyl)₄ ⁻ salts.Representative alkali or alkaline earth metal salts include sodium,lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, loweralkyl sulfonate, and aryl sulfonate.

The term “solvate” refers to forms of the compound that are associatedwith a solvent, usually by a solvolysis reaction. This physicalassociation may include hydrogen bonding. Conventional solvents includewater, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and thelike. The compounds of Formula (I) may be prepared, e.g., in crystallineform, and may be solvated. Suitable solvates include pharmaceuticallyacceptable solvates and further include both stoichiometric solvates andnon-stoichiometric solvates. In certain instances, the solvate will becapable of isolation, for example, when one or more solvent moleculesare incorporated in the crystal lattice of a crystalline solid.“Solvate” encompasses both solution-phase and isolable solvates.Representative solvates include hydrates, ethanolates, and methanolates.

The term “hydrate” refers to a compound which is associated with water.Typically, the number of the water molecules contained in a hydrate of acompound is in a definite ratio to the number of the compound moleculesin the hydrate. Therefore, a hydrate of a compound may be represented,for example, by the general formula R.x H₂O, wherein R is the compoundand wherein x is a number greater than 0. A given compound may form morethan one type of hydrates, including, e.g., monohydrates (x is 1), lowerhydrates (x is a number greater than 0 and smaller than 1, e.g.,hemihydrates (R.0.5H₂O)), and polyhydrates (x is a number greater than1, e.g., dihydrates (R.2H₂O) and hexahydrates (R.6H₂O)).

As used herein, the term “tautomer” includes two or moreinterconvertable forms resulting from at least one formal migration of ahydrogen atom and at least one change in valency (e.g., a single bond toa double bond, a triple bond to a double bond, or vice versa). The exactratio of the tautomers depends on several factors, includingtemperature, solvent, and pH. Tautomerizations (i.e., the reactionproviding a tautomeric pair) may be catalyzed by acid or base. Exemplarytautomerizations include keto- to -enol; amide- to -imide; lactam- to-lactim; enamine-to-imine; and enamine- to-(a different) enaminetautomerizations.

It is also to be understood that compounds that have the same molecularformula but differ in the nature or sequence of bonding of their atomsor the arrangement of their atoms in space are termed “isomers”. Isomersthat differ in the arrangement of their atoms in space are termed“stereoisomers”.

Stereoisomers that are not mirror images of one another are termed“diastereomers” and those that are non-superimposable mirror images ofeach other are termed “enantiomers”. When a compound has an asymmetriccenter, for example, it is bonded to four different groups, a pair ofenantiomers is possible. An enantiomer can be characterized by theabsolute configuration of its asymmetric center and is described by theR- and S-sequencing rules of Cahn and Prelog, or by the manner in whichthe molecule rotates the plane of polarized light and designated asdextrorotatory or levorotatory (i.e., as (+) or (−)-isomersrespectively). A chiral compound can exist as either individualenantiomer or as a mixture thereof. A mixture containing equalproportions of the enantiomers is called a “racemic mixture”.

The term “polymorphs” refers to a crystalline form of a compound (or asalt, hydrate, or solvate thereof) in a particular crystal packingarrangement. All polymorphs have the same elemental composition.Different crystalline forms usually have different X-ray diffractionpatterns, infrared spectra, melting points, density, hardness, crystalshape, optical and electrical properties, stability, and/or solubility.Recrystallization solvent, rate of crystallization, storage temperature,and other factors may cause one crystal form to dominate. Variouspolymorphs of a compound can be prepared by crystallization underdifferent conditions.

The term “prodrugs” refer to compounds, including derivatives of thecompounds of Formula (I), which have cleavable groups and are convertedby hydrolysis or under physiological conditions to the compounds ofFormula (I), which are pharmaceutically active in vivo. Such examplesinclude, but are not limited to, choline ester derivatives and the like,N-alkylmorpholine esters and the like. Other derivatives of thecompounds of this invention have activity in both their acid and acidderivative forms, but in the acid-sensitive form often offers advantagesof solubility, tissue compatibility, or delayed release in the mammalianorganism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24,Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well knownto practitioners of the art, such as, for example, esters prepared byreaction of the parent acid with a suitable alcohol, or amides preparedby reaction of the parent acid compound with a substituted orunsubstituted amine, or acid anhydrides, or mixed anhydrides. Simplealiphatic or aromatic esters, amides, and anhydrides derived from acidicgroups pendant on the compounds of this invention are particularprodrugs. In some cases it is desirable to prepare double ester typeprodrugs such as (acyloxy)alkyl esters or((alkoxycarbonyl)oxy)alkylesters. C₁ to C₈ alkyl, C₂-C₈ alkenyl, C₂-C₈alkynyl, aryl, C₇-C₁₂ substituted aryl, and C₇-C₁₂ arylalkyl esters ofthe compounds of Formula (I) may be preferred in certain instances.

A “subject” to which administration is contemplated includes, but is notlimited to, humans (i.e., a male or female of any age group, e.g., apediatric subject (e.g., infant, child, adolescent) or adult subject(e.g., young adult, middle-aged adult, or senior adult)) and/or othernon-human animals, for example, mammals (e.g., primates (e.g.,cynomolgus monkeys, rhesus monkeys); commercially relevant mammals suchas cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds(e.g., commercially relevant birds such as chickens, ducks, geese,and/or turkeys). In certain embodiments, the animal is a mammal. Theanimal may be a male or female and at any stage of development. Anon-human animal may be a transgenic animal.

The terms “administer,” “administering,” or “administration,” as usedherein refers to implanting, absorbing, ingesting, injecting, inhaling,or otherwise introducing an inventive compound, or a pharmaceuticalcomposition thereof.

As used herein, the terms “treatment,” “treat,” and “treating” refer toreversing, alleviating, delaying the onset of, or inhibiting theprogress of a “pathological condition” (e.g., a disease, disorder, orcondition, or one or more signs or symptoms thereof) described herein.In some embodiments, treatment may be administered after one or moresigns or symptoms have developed or have been observed. In otherembodiments, treatment may be administered in the absence of signs orsymptoms of the disease or condition. For example, treatment may beadministered to a susceptible individual prior to the onset of symptoms(e.g., in light of a history of symptoms and/or in light of genetic orother susceptibility factors). Treatment may also be continued aftersymptoms have resolved, for example, to delay or prevent recurrence.

As used herein, the terms “condition,” “disease,” and “disorder” areused interchangeably.

An “effective amount” of a compound of Formulae (I)-(VI) refers to anamount sufficient to elicit a desired biological response, i.e.,treating the condition. As will be appreciated by those of ordinaryskill in this art, the effective amount of a compound of Formulae(I)-(VI) may vary depending on such factors as the desired biologicalendpoint, the pharmacokinetics of the compound, the condition beingtreated, the mode of administration, and the age and health of thesubject. An effective amount encompasses therapeutic and prophylactictreatment. For example, in treating cancer, an effective amount of aninventive compound may reduce the tumor burden or stop the growth orspread of a tumor. In treating macular degeneration, an effective amountof an inventive compound may improve sight, reduce the risk of visionloss, or prevent central vision loss from worsening.

A “therapeutically effective amount” of a compound of Formulae (I)-(VI)is an amount sufficient to provide a therapeutic benefit in thetreatment of a condition or to delay or minimize one or more symptomsassociated with the condition. A therapeutically effective amount of acompound means an amount of therapeutic agent, alone or in combinationwith other therapies, which provides a therapeutic benefit in thetreatment of the condition. The term “therapeutically effective amount”can encompass an amount that improves overall therapy, reduces or avoidssymptoms or causes of the condition, or enhances the therapeuticefficacy of another therapeutic agent.

A “prophylactically effective amount” of a compound of Formula (I)-(VI)is an amount sufficient to prevent a condition, or one or more symptomsassociated with the condition or prevent its recurrence. Aprophylactically effective amount of a compound means an amount of atherapeutic agent, alone or in combination with other agents, whichprovides a prophylactic benefit in the prevention of the condition. Theterm “prophylactically effective amount” can encompass an amount thatimproves overall prophylaxis or enhances the prophylactic efficacy ofanother prophylactic agent.

A “proliferative disease” refers to a disease that occurs due toabnormal growth or extension by the multiplication of cells (Walker,Cambridge Dictionary of Biology; Cambridge University Press: Cambridge,UK, 1990). A proliferative disease may be associated with: 1) thepathological proliferation of normally quiescent cells; 2) thepathological migration of cells from their normal location (e.g.,metastasis of neoplastic cells); 3) the pathological expression ofproteolytic enzymes such as matrix metalloproteinases (e.g.,collagenases, gelatinases, and elastases); or 4) pathologicalangiogenesis as in proliferative retinopathy and tumor metastasis.Exemplary proliferative diseases include cancers (i.e., “malignantneoplasms”), benign neoplasms, angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases.

The terms “neoplasm” and “tumor” are used herein interchangeably andrefer to an abnormal mass of tissue wherein the growth of the masssurpasses and is not coordinated with the growth of a normal tissue. Aneoplasm or tumor may be “benign” or “malignant,” depending on thefollowing characteristics: degree of cellular differentiation (includingmorphology and functionality), rate of growth, local invasion, andmetastasis. A “benign neoplasm” is generally well differentiated, hascharacteristically slower growth than a malignant neoplasm, and remainslocalized to the site of origin. In addition, a benign neoplasm does nothave the capacity to infiltrate, invade, or metastasize to distantsites. Exemplary benign neoplasms include, but are not limited to,lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheickeratoses, lentigos, and sebaceous hyperplasias. In some cases, certain“benign” tumors may later give rise to malignant neoplasms, which mayresult from additional genetic changes in a subpopulation of the tumor'sneoplastic cells, and these tumors are referred to as “pre-malignantneoplasms.” An example of a pre-malignant neoplasm is a teratoma. Incontrast, a “malignant neoplasm” is generally poorly differentiated(anaplasia) and has characteristically rapid growth accompanied byprogressive infiltration, invasion, and destruction of the surroundingtissue. Furthermore, a malignant neoplasm generally has the capacity tometastasize to distant sites.

The term “metastasis,” “metastatic,” or “metastasize” refers to thespread or migration of cancerous cells from a primary or original tumorto another organ or tissue and is typically identifiable by the presenceof a “secondary tumor” or “secondary cell mass” of the tissue type ofthe primary or original tumor and not of that of the organ or tissue inwhich the secondary (metastatic) tumor is located. For example, aprostate cancer that has migrated to bone is said to be metastasizedprostate cancer and includes cancerous prostate cancer cells growing inbone tissue.

As used herein, the term “cancer” refers to a malignant neoplasm(Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins:Philadelphia, 1990). Exemplary cancers include, but are not limited to,acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer;angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma,hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliarycancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g.,adenocarcinoma of the breast, papillary carcinoma of the breast, mammarycancer, medullary carcinoma of the breast); brain cancer (e.g.,meningioma, glioblastomas, glioma (e.g., astrocytoma,oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor;cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma;chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer,rectal cancer, colorectal adenocarcinoma); connective tissue cancer;epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi'ssarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer(e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g.,adenocarcinoma of the esophagus, Barrett's adenocarinoma); Ewing'ssarcoma; eye cancer (e.g., intraocular melanoma, retinoblastoma);familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g.,stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germcell cancer; head and neck cancer (e.g., head and neck squamous cellcarcinoma, oral cancer (e.g., oral squamous cell carcinoma), throatcancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngealcancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemiasuch as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL),acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronicmyelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chroniclymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphomasuch as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) andnon-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large celllymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicularlymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma(CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas(e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodalmarginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma),primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacyticlymphoma (i.e., Waldenstrom's macroglobulinemia), hairy cell leukemia(HCL), immunoblastic large cell lymphoma, precursor B-lymphoblasticlymphoma and primary central nervous system (CNS) lymphoma; and T-cellNHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheralT-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g.,mycosis fungiodes, Sezary syndrome), angioimmunoblastic T-cell lymphoma,extranodal natural killer T-cell lymphoma, enteropathy type T-celllymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplasticlarge cell lymphoma); a mixture of one or more leukemia/lymphoma asdescribed above; and multiple myeloma (MM)), heavy chain disease (e.g.,alpha chain disease, gamma chain disease, mu chain disease);hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastictumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastomaa.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g.,hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g.,bronchogenic carcinoma, small cell lung cancer (SCLC), non-small celllung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS);mastocytosis (e.g., systemic mastocytosis); muscle cancer;myelodysplastic syndrome (MDS); mesothelioma; myeloproliferativedisorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis(ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF),chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML),chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES));neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreaticneuroendoctrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g.,bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarianembryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma;pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductalpapillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer(e.g., Paget's disease of the penis and scrotum); pinealoma; primitiveneuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplasticsyndromes; intraepithelial neoplasms; prostate cancer (e.g., prostateadenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer;skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA),melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g.,appendix cancer); soft tissue sarcoma (e.g., malignant fibroushistiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor(MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous glandcarcinoma; small intestine cancer; sweat gland carcinoma; synovioma;testicular cancer (e.g., seminoma, testicular embryonal carcinoma);thyroid cancer (e.g., papillary carcinoma of the thyroid, papillarythyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer;vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).

The term “angiogenesis” refers to the formation and growth of new bloodvessels. Normal angiogenesis occurs in the healthy body of a subjectduring wound healing and for restoring blood flow to tissues afterinjury. The healthy body controls angiogenesis through a number ofmeans, e.g., angiogenesis-stimulating growth factors and angiogenesisinhibitors. Many disease states, such as cancer, diabetic blindness,age-related macular degeneration, rheumatoid arthritis, and psoriasis,are characterized by abnormal (i.e., increased or excessive)angiogenesis. Abnormal angiogenesis refers to angiogenesis greater thanthat in a normal body, especially angiogenesis in an adult not relatedto normal angiogenesis (e.g., menstruation or wound healing). Abnormalangiogenesis can result in new blood vessels that feed diseased tissuesand/or destroy normal tissues, and in the case of cancer, the newvessels can allow tumor cells to escape into the circulation and lodgein other organs (tumor metastases).

As used herein, an “inflammatory disease” refers to a disease caused by,resulting from, or resulting in inflammation. The term “inflammatorydisease” may also refer to a dysregulated inflammatory reaction thatcauses an exaggerated response by macrophages, granulocytes, and/orT-lymphocytes leading to abnormal tissue damage and/or cell death. Aninflammatory disease can be either an acute or chronic inflammatorycondition and can result from infections or non-infectious causes.Inflammatory diseases include, without limitation, atherosclerosis,arteriosclerosis, autoimmune disorders, multiple sclerosis, systemiclupus erythematosus, polymyalgia rheumatica (PMR), gouty arthritis,degenerative arthritis, tendonitis, bursitis, psoriasis, cysticfibrosis, arthrosteitis, rheumatoid arthritis, inflammatory arthritis,Sjogren's syndrome, giant cell arteritis, progressive systemic sclerosis(scleroderma), ankylosing spondylitis, polymyositis, dermatomyosifis,pemphigus, pemphigoid, diabetes (e.g., Type I), myasthenia gravis,Hashimoto's thyroditis, Graves' disease, Goodpasture's disease, mixedconnective tissue disease, sclerosing cholangitis, inflammatory boweldisease, Crohn's disease, ulcerative colitis, pernicious anemia,inflammatory dermatoses, usual interstitial pneumonitis (UIP),asbestosis, silicosis, bronchiectasis, berylliosis, talcosis,pneumoconiosis, sarcoidosis, desquamative interstitial pneumonia,lymphoid interstitial pneumonia, giant cell interstitial pneumonia,cellular interstitial pneumonia, extrinsic allergic alveolitis,Wegener's granulomatosis and related forms of angiitis (temporalarteritis and polyarteritis nodosa), inflammatory dermatoses, hepatitis,delayed-type hypersensitivity reactions (e.g., poison ivy dermatitis),pneumonia, respiratory tract inflammation, Adult Respiratory DistressSyndrome (ARDS), encephalitis, immediate hypersensitivity reactions,asthma, hayfever, allergies, acute anaphylaxis, rheumatic fever,glomerulonephritis, pyelonephritis, cellulitis, cystitis, chroniccholecystitis, ischemia (ischemic injury), reperfusion injury, allograftrejection, host-versus-graft rejection, appendicitis, arteritis,blepharitis, bronchiolitis, bronchitis, cervicitis, cholangitis,chorioamnionitis, conjunctivitis, dacryoadenitis, dermatomyositis,endocarditis, endometritis, enteritis, enterocolitis, epicondylitis,epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis,gingivitis, ileitis, iritis, laryngitis, myelitis, myocarditis,nephritis, omphalitis, oophoritis, orchitis, osteitis, otitis,pancreatitis, parotitis, pericarditis, pharyngitis, pleuritis,phlebitis, pneumonitis, proctitis, prostatitis, rhinitis, salpingitis,sinusitis, stomatitis, synovitis, testitis, tonsillitis, urethritis,urocystitis, uveitis, vaginitis, vasculitis, vulvitis, vulvovaginitis,angitis, chronic bronchitis, osteomylitis, optic neuritis, temporalarteritis, transverse myelitis, necrotizing fascilitis, and necrotizingenterocolitis.

As used herein, an “autoimmune disease” refers to a disease arising froman inappropriate immune response in the body of a subject againstsubstances and tissues normally present in the body. In other words, theimmune system mistakes some part of the body as a pathogen and attacksits own cells. This may be restricted to certain organs (e.g., inautoimmune thyroiditis) or involve a particular tissue in differentplaces (e.g., Goodpasture's disease which may affect the basementmembrane in both the lung and kidney). The treatment of autoimmunediseases is typically with immunosuppressants, e.g., medications whichdecrease the immune response. Exemplary autoimmune diseases include, butare not limited to, glomerulonephritis, Goodspature's syndrome,necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemiclupus erythematosis, rheumatoid, arthritis, psoriatic arthritis,systemic lupus erythematosis, psoriasis, ulcerative colitis, systemicsclerosis, dermatomyositis/polymyositis, anti-phospholipid antibodysyndrome, scleroderma, perphigus vulgaris, ANCA-associated vasculitis(e.g., Wegener's granulomatosis, microscopic polyangiitis), urveitis,Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosingspondylitis, Lyme arthritis, Guillain-Barre syndrome, Hashimoto'sthyroiditis, and cardiomyopathy.

The term “autoinflammatory disease” refers to a category of diseasesthat are similar but different from autoimmune diseases.Autoinflammatory and autoimmune diseases share common characteristics inthat both groups of disorders result from the immune system attacking asubject's own tissues and result in increased inflammation. Inautoinflammatory diseases, a subject's innate immune system causesinflammation for unknown reasons. The innate immune system reacts eventhough it has never encountered autoantibodies or antigens in thesubject. Autoinflammatory disorders are characterized by intenseepisodes of inflammation that result in such symptoms as fever, rash, orjoint swelling. These diseases also carry the risk of amyloidosis, apotentially fatal buildup of a blood protein in vital organs.Autoinflammatory diseases include, but are not limited to, familialMediterranean fever (FMF), neonatal onset multisystem inflammatorydisease (NOMID), tumor necrosis factor (TNF) receptor-associatedperiodic syndrome (TRAPS), deficiency of the interleukin-1 receptorantagonist (DIRA), and Behçet's disease.

The term “biological sample” refers to any sample including tissuesamples (such as tissue sections and needle biopsies of a tissue); cellsamples (e.g., cytological smears (such as Pap or blood smears) orsamples of cells obtained by microdissection); samples of wholeorganisms (such as samples of yeasts or bacteria); or cell fractions,fragments or organelles (such as obtained by lysing cells and separatingthe components thereof by centrifugation or otherwise). Other examplesof biological samples include blood, serum, urine, semen, fecal matter,cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus,biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy),nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccalswabs), or any material containing biomolecules that is derived from afirst biological sample. Biological samples also include thosebiological samples that are transgenic, such as transgenic oocyte, spermcell, blastocyst, embryo, fetus, donor cell, or cell nucleus.

A “protein” or “peptide” comprises a polymer of amino acid residueslinked together by peptide bonds. The term, as used herein, refers toproteins, polypeptides, and peptides of any size, structure, orfunction. Typically, a protein will be at least three amino acids long.A protein may refer to an individual protein or a collection ofproteins. Inventive proteins preferably contain only natural aminoacids, although non-natural amino acids (i.e., compounds that do notoccur in nature but that can be incorporated into a polypeptide chain)and/or amino acid analogs as are known in the art may alternatively beemployed. Also, one or more of the amino acids in an inventive proteinmay be modified, for example, by the addition of a chemical entity suchas a carbohydrate group, a hydroxyl group, a phosphate group, a farnesylgroup, an isofarnesyl group, a fatty acid group, a linker forconjugation or functionalization, or other modification. A protein mayalso be a single molecule or may be a multi-molecular complex. A proteinmay be a fragment of a naturally occurring protein or peptide. A proteinmay be naturally occurring, recombinant, or synthetic, or anycombination of these.

The term “kinase” refers to any enzyme that catalyzes the addition of aphosphate group to a residue of a protein. For example, a serine kinasecatalyzes the addition of a phosphate group to a serine residue of aprotein.

The term “ocular disease” or “ocular disorder” refers to any eye diseaseand/or disorder. For example, ocular diseases can be disorders of theeyelid, lacrimal system and orbit, disorders of conjunctiva, disordersof sclera, cornea, iris and ciliary body, disorders of choroid andretina, glaucoma, disorders of optic nerve and visual pathways, ordisorders of ocular muscles. Additionally, ocular disease can also referto discomfort following injury, surgery, or laser treatment. Diseasesand disorders of the eye include, but are not limited to, maculardegeneration, dry eye syndrome, uveitis, allergic conjunctivitis,glaucoma, and rosacea (of the eye). Dry eye syndrome (DES), otherwiseknown as keratoconjunctivitis sicca (KCS), keratitis sicca, siccasyndrome, or xerophthalmia, is an eye disease caused by decreased tearproduction or increased tear film evaporation commonly found in humansand some animals. Uveitis or iridocyclitis refers to inflammation of themiddle layer of the eye (the “uvea”) and in common usage may refer toany inflammatory process involving the interior of the eye. Allergicconjunctivitis is inflammation of the conjunctiva (the membrane coveringthe white part of the eye) due to allergy. Glaucoma refers to a group ofdiseases that affect the optic nerve and involves a loss of retinalganglion cells in a characteristic pattern, i.e., a type of opticneuropathy. Raised intraocular pressure is a significant risk factor fordeveloping glaucoma (above 22 mmHg or 2.9 kPa), and inflammatoryprocesses, e.g.I, uveitis, can cause this rise in intraocular pressure.Rosacea is a chronic inflammatory condition characterized by facialerythema but it can affect the eyes.

The terms “macular degeneration,” “age-related macular degeneration,”“dry AMD,” and “central geographic atrophy” are used interchangeablyherein. These terms refer to diseases that result from atrophy of theretinal pigment epithelial layer below the neurosensory retina, whichcauses vision loss through loss of photoreceptors (rods and cones) inthe central part of the retinal.

The term “VEGF” is used interchangeably with vascular endothelial growthfactor herein. It includes but is not limited to VEGF-related proteinssuch as Placenta growth factor (PGF), VEGF-A, VEGF-B, VEGF-C, VEGF-D,VEGF-E, and VEGF-F. The term VEGF also covers a number of proteins fromtwo families that result from alternate splicing of mRNA from a single,8-exon, VEGF gene. The two different families are referred to accordingto their terminal exon (exon 8) splice site—the proximal splice site(denoted VEGF_(xxx)) or distal splice site (VEGF_(xxxb)). In addition,alternate splicing of exon 6 and 7 alters their heparin-bindingaffinity, and amino acid number (in humans: VEGF₁₂₁, VEGF_(121b),VEGF₁₄₅, VEGF₁₆₅, VEGF_(165b), VEGF₁₈₉, VEGF₂₀₆; the rodent orthologs ofthese proteins contain one fewer amino acid). These domains haveimportant functional consequences for the VEGF splice variants, as theterminal (exon 8) splice site determines whether the proteins arepro-angiogenic (proximal splice site, expressed during angiogenesis) oranti-angiogenic (distal splice site, expressed in normal tissues). Inaddition, inclusion or exclusion of exons 6 and 7 mediate interactionswith heparan sulfate proteoglycans (HSPGs) and neuropilin co-receptorson the cell surface, enhancing their ability to bind and activate theVEGF receptors (VEGFRs). The term “VEGF” also encompasses VEGFreceptors. There are three main subtypes of VEGFR, numbered 1, 2 and 3.Also, they may be membrane-bound (mbVEGFR) or soluble (sVEGFR),depending on alternative splicing.

The term “particle” refers to a small object, fragment, or piece of asubstance that may be a single element, inorganic material, organicmaterial, or mixture thereof. Examples of particles include polymericparticles, single-emulsion particles, double-emulsion particles,coacervates, liposomes, microparticles, nanoparticles, macroscopicparticles, pellets, crystals (e.g., crystalline forms of compounds oractive pharmaceutical agent), aggregates, composites, pulverized,milled, or otherwise disrupted matrices, and cross-linked protein orpolysaccharide particles, each of which have an average characteristicdimension of about less than about 1 mm and at least 1 nm, where thecharacteristic dimension, or “critical dimension,” of the particle isthe smallest cross-sectional dimension of the particle. A particle maybe composed of a single substance or multiple substances. In certainembodiments, the particle is not a viral particle. In other embodiments,the particle is not a liposome. In certain embodiments, the particle isnot a micelle. In certain embodiments, the particle is substantiallysolid throughout. In certain embodiments, the particle is ananoparticle. In certain embodiments, the particle is a microparticle.

The term “nanoparticle” refers to a particle having a characteristicdimension of less than about 1 micrometer and at least about 1nanometer, where the characteristic dimension of the particle is thesmallest cross-sectional dimension of the particle. A crystallinenanoparticle is referred to as a “nanocrystal.”

The term “microparticle” refers to a particle having a characteristicdimension of less than about 1 millimeter and at least about 1micrometer, where the characteristic dimension of the particle is thesmallest cross-sectional dimension of the particle.

The term “nanostructure” refers to a structure having at least oneregion or characteristic dimension with a dimension of less than about1000 nm, e.g., less than about 300 nm, less than about 200 nm, less thanabout 100 nm, or less than about 50 nm. Typically, the region orcharacteristic dimension will be along the smallest axis of thestructure. Examples of such structures include nanowires, nanorods,nanotubes, branched nanocrystals, nanotetrapods, tripods, bipods,nanocrystals, nanodots, quantum dots, nanoparticles, branched tetrapods(e.g., inorganic dendrimers), and the like. Nanostructures can besubstantially homogeneous in material properties, or in certainembodiments can be heterogeneous (e.g. heterostructures). Nanostructurescan be, e.g., substantially crystalline, substantially monocrystalline,polycrystalline, amorphous, or a combination thereof. In one aspect,each of the three dimensions of the nanostructure has a dimension ofless than about 1000 nm, e.g., or even less than about 300 nm, less thanabout 200 nm, less than about 100 nm, or less than about 50 nm.Nanostructures can comprise one or more surface ligands (e.g.,surfactants).

The terms “crystalline” or “substantially crystalline”, when used withrespect to nanostructures, refer to the fact that the nanostructurestypically exhibit long-range ordering across one or more dimensions ofthe structure. It will be understood by one of skill in the art that theterm “long range ordering” will depend on the absolute size of thespecific nanostructures, as ordering for a single crystal cannot extendbeyond the boundaries of the crystal. In this case, “long-rangeordering” will mean substantial order across at least the majority ofthe dimension of the nanostructure. In some instances, a nanostructurecan bear an oxide or other coating, or can be comprised of a core and atleast one shell. In such instances it will be appreciated that theoxide, shell(s), or other coating need not exhibit such ordering (e.g.it can be amorphous, polycrystalline, or otherwise). In such instances,the phrase “crystalline,” “substantially crystalline,” “substantiallymonocrystalline,” or “monocrystalline” refers to the central core of thenanostructure (excluding the coating layers or shells). The terms“crystalline” or “substantially crystalline” as used herein are intendedto also encompass structures comprising various defects, stackingfaults, atomic substitutions, and the like, as long as the structureexhibits substantial long range ordering (e.g., order over at leastabout 80% of the length of at least one axis of the nano structure orits core). In addition, it will be appreciated that the interfacebetween a core and the outside of a nanostructure or between a core andan adjacent shell or between a shell and a second adjacent shell maycontain non-crystalline regions and may even be amorphous. This does notprevent the nanostructure from being crystalline or substantiallycrystalline as defined herein. The term “monocrystalline” when used withrespect to a nanostructure indicates that the nanostructure issubstantially crystalline and comprises substantially a single crystal.When used with respect to a nanostructure heterostructure comprising acore and one or more shells, “monocrystalline” indicates that the coreis substantially crystalline and comprises substantially a singlecrystal. When not used with respect to a nanostructure, the term“monocrystalline” to materials that are composed of substantially asingle crystallite of substantially the same size and orientation.

“Nanocrystal” is a nanostructure that is substantially monocrystalline.A nanocrystal thus has at least one region or characteristic dimensionwith a dimension of less than about 1000 nm, e.g., less than about 300nm less than about 200 nm, less than about 100 nm, or less than about 50nm. Typically, the region or characteristic dimension will be along thesmallest axis of the structure. Examples of such structures includenanowires, nanorods, nanotubes, branched nanowires, nanotetrapods,nanotripods, nanobipods, nanocrystals, nanodots, quantum dots,nanoparticles, nanoribbons, and the like. Nanostructures can besubstantially homogeneous in material properties, or in certainembodiments can be heterogeneous (e.g. heterostructures). Optionally, ananocrystal can comprise one or more surface ligands (e.g.,surfactants). The nanocrystal is optionally substantially single crystalin structure (a “single crystal nanostructure” or a “monocrystallinenanostructure”). While nanostructures for use in the present inventioncan be fabricated from essentially any convenient material or material,preferably the nanostructure is prepared from an inorganic material,e.g., an inorganic conductive or semiconductive material. A conductiveor semi-conductive nanostructure often displays 1-dimensional quantumconfinement, e.g., an electron can often travel along only one dimensionof the structure. Nanocrystals can be substantially homogeneous inmaterial properties, or in certain embodiments can be heterogeneous(e.g. heterostructures). The term “nanocrystal” is intended to encompasssubstantially monocrystalline nanostructures comprising various defects,stacking faults, atomic substitutions, and the like, as well assubstantially monocrystalline nanostructures without such defects,faults, or substitutions. In the case of nanocrystal heterostructurescomprising a core and one or more shells, the core of the nanocrystal istypically substantially monocrystalline, but the shell(s) need not be.The nanocrystals can be fabricated from essentially any convenientmaterial or materials.

The term “polycrystalline” refers to materials that are composed of manycrystallites of varying size and orientation. When used with respect tonanostructures, the term “polycrystalline” refers to a crystallinenanostructure that is not monocrystalline.

A “biocompatible” material refers to a material that does not typicallyinduce an adverse response when inserted or injected into a subject. Theadverse response includes significant inflammation and/or acuterejection of the material by the immune system of the subject, forinstance, via a T-cell-mediated response. It is recognized that“biocompatibility” is a relative term and that some degree of immuneresponse is to be expected even for materials that are highly compatiblewith living tissues of the subject. However, as used herein,“biocompatibility” refers to the acute rejection of a material by atleast a portion of the immune system, i.e., a material that lacksbiocompatibility (i.e. being non-biocompatible) in a subject provokes animmune response in the subject that is severe enough such that therejection of the material by the immune system cannot be adequatelycontrolled and often is of a degree such that the material must beremoved from the subject in order for the subject to be as well as itwas before the non-biocompatible material was introduced into thesubject. One test to determine biocompatibility of a material is toexpose the material to cells (e.g., fibroblasts or epithelial cells) invitro; the material is considered biocompatible if it does not result insignificant cell death at moderate concentrations, e.g., atconcentrations of about 50 micrograms/10⁶ cells. In certain embodiments,there is no significant cell death if less than about 20% of the cellsare dead, even if phagocytosed or otherwise uptaken by the cells. Insome embodiments, a material is biocompatible if contacting it withcells in vitro results in less than 20% cell death and if theadministration of the material in vivo does not induce unwantedinflammation or other adverse responses. In certain embodiments, abiocompatible material is biodegradable. A non-limiting example ofbiocompatible materials is biocompatible polymers (includingbiocompatible copolymers).

A “biodegradable” material refers to a material that is able to degradechemically and/or biologically (e.g., by hydrolysis or enzymaticactivity), within a physiological environment, such as within the bodyor when introduced to cells. For instance, the material may be one thathydrolyzes spontaneously upon exposure to water (e.g., within a subject)and/or may degrade upon exposure to heat (e.g., at temperatures of about37° C.). Degradation of a material may occur at varying rates, dependingon the material used. For example, the half-life of the material (thetime at which 50% of the material is degraded into smaller components)may be on the order of days, weeks, months, or years. The material maybe biologically degraded, e.g., by enzymatic activity or cellularmachinery, for example, through exposure to a lysozyme. In someembodiments, the material may be broken down into smaller componentsthat cells can either reuse or dispose of without significant toxiceffect on the cells (e.g., fewer than about 20% of the cells are killedwhen the components are added to cells in vitro). Non-limiting examplesof biodegradable materials are biodegradable polymers (includingbiodegradable copolymers). Examples of biodegradable polymers include,but are not limited to, poly(ethylene glycol)-poly(propyleneoxide)-poly(ethylene glycol) triblock copolymers, poly(vinyl alcohol)(PVA), poly(lactide) (or poly(lactic acid)), poly(glycolide) (orpoly(glycolic acid)), poly(orthoesters), poly(caprolactones),polylysine, poly(ethylene imine), poly(acrylic acid), poly(urethanes),poly(anhydrides), poly(esters), poly(trimethylene carbonate),poly(ethyleneimine), poly(acrylic acid), poly(urethane), poly(beta aminoesters), and copolymers thereof (e.g., poly(lactide-co-glycolide)(PLGA)).

As used herein, the terms “pharmaceutical composition” and “formulation”are used interchangeably.

As used herein, the terms “pharmaceutical agent” and “drug” are usedinterchangeably.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS

The present invention provides compounds of Formulae (I)-(VI). Alsoprovided are methods of using compounds of Formulae (I)-(VI), to treatproliferative diseases, ocular diseases, dermatological diseases,inflammation diseases, or metabolic diseases. The present inventionfurther provides methods of using the compounds of Formulae (I)-(VI) astherapeutics, e.g., in the treatment and/or prevention of diseasesassociated with growth factor activities or angiogenesis. In certainembodiments, the disease being treated is a proliferative disease.Exemplary proliferative diseases include, but are not limited to,cancers, benign neoplasms, diseases associated with angiogenesis,inflammatory diseases, autoinflammatory diseases, and autoimmunediseases. In certain embodiments, the disease is an ocular disease.Exemplary ocular diseases include, but are not limited to, maculardegeneration, dry eye syndrome, uveitis, allergic conjunctivitis,glaucoma, and rosacea.

Compounds

As generally described herein, the present disclosure provides compoundsof Formula (I):

wherein:

R₁ is independently hydrogen or optionally substituted C₁₋₆ alkyl;

R₂ is optionally hydrogen, substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl;

X is a bond, —O—, —S—, NR^(A1)—, —C(═O)—, or branched or unbranchedoptionally substituted C₁₋₆ alkylene, wherein R^(A1) is independentlyhydrogen, optionally substituted acyl, optionally substituted alkyl, ora nitrogen protecting group;

Y is N or CH;

each instance of R₃ is independently selected from the group consistingof hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CN, —NO₂, —OR^(D1a), —N(R^(D1a))₂, —SR^(D1a),—CH₂OR^(D1a), —CH₂N(R^(D1a))₂, —CH₂SR^(D1a), —C(═O)R^(D1a),—C(═O)OR^(D1a), —C(═O)SR^(D1a), —C(═O)N(R^(D1a))₂, —C(═S)R^(D1a),—C(═S)OR^(D1a), —C(═S)SR^(D1a), —C(═S)N(R^(D1a))₂, —C(═NR^(D1a))R^(D1a),—C(═NR^(D1a))OR^(D1a), —C(═NR^(D1a))SR^(D1a), andC(═NR^(D1a))N(R^(D1a))₂, wherein each occurrence of R^(D1a) isindependently selected from the group consisting of hydrogen, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(D1a) groups are joined to form anoptionally substituted heterocyclic ring;

Z is independently optionally substituted aliphatic, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, optionally substituted heterocyclylalkyl,optionally substituted arylalkyl, optionally substituted heteroaralkyl,or optionally substituted quinolyl;

m is 0, 1, 2, 3, or 4; and

n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In another aspect, the present disclosure provides compounds of Formula(VI):

wherein:

R₁ is independently hydrogen or optionally substituted C₁₋₆ alkyl;

R₂ is optionally hydrogen, substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl;

X is a bond, —O—, —S—, NR^(A1)—, —C(═O)—, or branched or unbranchedoptionally substituted C₁₋₆ alkylene, wherein R^(A1) is independentlyhydrogen, optionally substituted acyl, optionally substituted alkyl, ora nitrogen protecting group;

Y is N or CH;

each instance of R₃ is independently selected from the group consistingof hydrogen, halogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CN, —NO₂, —OR^(D1a), —N(R^(D1a))₂, —SR^(D1a),—CH₂OR^(D1a), —CH₂N(R^(D1a))₂, —CH₂SR^(D1a), —C(═O)R^(D1a),—C(═O)OR^(D1a), —C(═O)SR^(D1a), —C(═O)N(R^(D1a))₂, —C(═S)R^(D1a),—C(═S)OR^(D1a), —C(═S)SR^(D1a), —C(═S)N(R^(D1a))₂, —C(═NR^(D1a))R^(D1a),—C(═NR^(D1a))OR^(D1a), —C(═NR^(D1a))SR^(D1a), andC(═NR^(D1a))N(R^(D1a))₂, wherein each occurrence of R^(D1a) isindependently selected from the group consisting of hydrogen, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, and optionallysubstituted heteroaryl, or two R^(D1a) groups are joined to form anoptionally substituted heterocyclic ring;

Z is independently optionally substituted aliphatic, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, optionally substituted heterocyclylalkyl,optionally substituted arylalkyl, optionally substituted heteroaralkyl,or optionally substituted quinolyl;

m is 0, 1, 2, 3, or 4; and

n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

As generally described above, Z is independently optionally substitutedaliphatic, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, optionally substitutedheterocyclylalkyl, optionally substituted arylalkyl, optionallysubstituted heteroaralkyl, or optionally substituted quinolyl. Incertain embodiments, Z is optionally substituted, acyclic or cyclic C₁₋₆alkyl. In certain embodiments, Z is optionally substituted acyclic C₁₋₆alkyl. In certain embodiments, Z is optionally substituted cyclic C₁₋₆alkyl. In certain embodiments, Z is substituted C₁₋₆ alkyl. In certainembodiments, Z is unsubstituted C₁₋₆ alkyl. In certain embodiments, Z issubstituted methyl. In certain embodiments, Z is unsubstituted methyl.In certain embodiments, Z is substituted ethyl. In certain embodiments,Z is unsubstituted ethyl. In certain embodiments, Z is substitutedpropyl. In certain embodiments, Z is unsubstituted propyl. In certainembodiments, Z is substituted n-propyl. In certain embodiments, Z isunsubstituted n-propyl. In certain embodiments, Z is substitutediso-propyl. In certain embodiments, Z is unsubstituted iso-propyl. Incertain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

As used above, g is 0, 1, 2, 3, 4, 5, 6, 7, or 8. In certainembodiments, g is 0. In certain embodiments, g is 1. In certainembodiments, g is 2. In certain embodiments, g is 3. In certainembodiments, g is 4. In certain embodiments, g is 5. In certainembodiments, g is 6. In certain embodiments, g is 7. In certainembodiments, g is 8.

In certain embodiments, Z is optionally substituted heterocyclylalkyl.In certain embodiments, Z is optionally substituted heterocyclylalkylwith one nitrogen. In certain embodiments, Z is optionally substitutedheterocyclylalkyl with one oxygen. In certain embodiments, Z is of theformula

wherein h is 1, 2, 3, 4, 5, 6, 7 or 8, and each of e and f isindependently 1, 2, or 3. In certain embodiments, h is 1. In certainembodiments, h is 2. In certain embodiments, h is 3. In certainembodiments, h is 4. In certain embodiments, h is 5. In certainembodiments, h is 6. In certain embodiments, h is 7. In certainembodiments, h is 8. In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is optionally substituted aryl. In certainembodiments, Z is optionally substituted monocyclic aryl. In certainembodiments, Z is of the formula

Each instance of R₅ is independently hydrogen, halogen, optionallysubstituted alkyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(5A), —N(R^(5A))₂, —SR^(5A), —CN,—C(═O)R^(5A), —C(═O)OR^(5A), —C(═O)N(R^(5A))₂, —NO₂, —N₃, —N(R^(5A))₃⁺X⁻, wherein X⁻ is a counterion, —OC(═O)R^(5A), or —OC(═O)OR^(5A), ortwo R⁵ groups are joined to form an optionally substituted carbocyclic,optionally substituted heterocyclic, optionally substituted aryl, oroptionally substituted heteroaryl ring; wherein each occurrence ofR^(5A) is independently hydrogen, optionally substituted acyl,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, or an oxygen protecting group when attached to an oxygenatom, or two R^(5A) groups are joined to form an optionally substitutedheterocyclic ring; and k is 0, 1, 2, 3, 4, or 5. In certain embodiments,k is 0. In certain embodiments, k is 1. In certain embodiments, k is 2.In certain embodiments, k is 3. In certain embodiments, k is 4. Incertain embodiments, k is 5. In certain embodiments, R₅ is hydrogen. Incertain embodiments, R₅ is optionally substituted, branched orunbranched C₁₋₆ alkyl. In certain embodiments, R₅ is unsubstitutedmethyl. In certain embodiments, R₅ is substituted methyl. In certainembodiments, R₅ is trifluoromethyl. In certain embodiments, R₅ isunsubstituted ethyl. In certain embodiments, R₅ is substituted ethyl. Incertain embodiments, R₅ is optionally substituted propyl. In certainembodiments, R₅ is substituted n-propyl. In certain embodiments, R₅ isunsubstituted n-propyl. In certain embodiments, R₅ is substitutediso-propyl. In certain embodiments, R₅ is unsubstituted iso-propyl. Incertain embodiments, R₅ is halogen. In certain embodiments, R₅ is I. Incertain embodiments, R₅ is Br. In certain embodiments, R₅ is Cl. Incertain embodiments, R₅ is F. In certain embodiments, R₅ is NO₂. Incertain embodiments, R₅ is —OH. In certain embodiments, R₅ is

—CN. In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is optionally substituted heteroaryl. Incertain embodiments, Z is optionally substituted bicyclic heteroaryl. Incertain embodiments, Z is optionally substituted indole. In certainembodiments, Z is optionally substituted aza-indole. In certainembodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

Each instance of k is 0, 1, 2, 3, or 4. In certain embodiments, k is 0.In certain embodiments, k is 1, In certain embodiments, k is 2. Incertain embodiments, k is 3. In certain embodiments, k is 4. In certainembodiments, R₅ is hydrogen. In certain embodiments, R₅ is optionallysubstituted, branched or unbranched C₁₋₆ alkyl. In certain embodiments,R₅ is substituted methyl. In certain embodiments, R₅ is unsubstitutedmethyl. In certain embodiments, R₅ is substituted ethyl. In certainembodiments, R₅ is unsubstituted ethyl. In certain embodiments, R₅ isoptionally substituted propyl. In certain embodiments, R₅ is substitutedn-propyl. In certain embodiments, R₅ is unsubstituted n-propyl. Incertain embodiments, R₅ is substituted iso-propyl. In certainembodiments, R₅ is unsubstituted iso-propyl. In certain embodiments, R₅is halogen. In certain embodiments, R₅ is I. In certain embodiments, R₅is Br. In certain embodiments, R₅ is Cl. In certain embodiments, R₅ isF. In certain embodiments, R₅ is NO₂. In certain embodiments, R₅ is —OH.In certain embodiments, R₅ is hydrogen, methyl or F. In certainembodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is a 5-membered monocyclic heteroaryl ring,wherein one of the five ring carbon atoms is independently replaced bynitrogen, oxygen, or sulfur. In certain embodiments, Z is of theformula:

In certain embodiments, Z is a 5-membered monocyclic heteroaryl ring,wherein two of the five ring carbon atoms are independently replaced bynitrogen, oxygen, or sulfur. In certain embodiments, Z is one of theformula:

In certain embodiments, Z is of the formula:

In certain embodiments, Z is of the formula:

Each instance of R₄ is independently selected from the group consistingof hydrogen, halogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —OR^(4A),—N(R^(4A))², —SR^(4A), —CN, —C(═O)R^(4A), —C(═O)OR^(4A), —C(═O)SR^(4A),—C(═O)N(R^(4A))₂, —NO₂, —N₃, —N(R^(4A))₃ ⁺X⁻, wherein X⁻ is acounterion, or two R₄ groups are joined to form an optionallysubstituted carbocyclic, optionally substituted heterocyclic, optionallysubstituted aryl, or optionally substituted heteroaryl ring; whereineach occurrence of R^(4A) is independently selected from the groupconsisting of hydrogen, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, an oxygen protecting group when attached to an oxygenatom, and a sulfur protecting group when attached to a sulfur atom, ortwo R^(4A) groups are joined to form an optionally substitutedheterocyclic ring; and e is 0, 1, 2, 3, 4, or 5.

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, R₄ is hydrogen. In certain embodiments, R₄ isoptionally substituted, branched or unbranched alkyl. In certainembodiments, R₄ is optionally substituted, branched or unbranched C₁₋₆alkyl. In certain embodiments, R₄ is substituted ethyl. In certainembodiments, R₄ is unsubstituted ethyl. In certain embodiments, R₄ issubstituted methyl. In certain embodiments, R₄ is unsubstituted methyl.In certain embodiments, R₄ is halogen. In certain embodiments, R₄ is F.In certain embodiments, R₄ is Cl. In certain embodiments, R₄ is Br. Incertain embodiments, R₄ is I. In certain embodiments, j is 0. In certainembodiments, j is 1. In certain embodiments, j is 2. In certainembodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is of the formula

In certain embodiments, Z is optionally substituted quinolyl. In certainembodiments, Z is of the formula

Each instance of R₅ is independently hydrogen, halogen, optionallysubstituted alkyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —OR^(5A), SR^(5A), —CN, —C(═O)R^(5A),—C(═O)OR^(5A), —C(═O)N(R^(5A))₂, —NO₂, —N₃, —N(R^(5A))₃ ⁺X⁻, wherein X⁻is a counterion, —OC(═O)R^(5A), or —OC(═O)OR^(5A), or two R⁵ groups arejoined to form an optionally substituted carbocyclic, optionallysubstituted heterocyclic, optionally substituted aryl, or optionallysubstituted heteroaryl ring; wherein each occurrence of R^(5A) isindependently hydrogen, methyl, optionally substituted acyl, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, a nitrogen protecting group when attached to anitrogen atom, or an oxygen protecting group when attached to an oxygenatom, or two R^(5A) groups are joined to form an optionally substitutedheterocyclic ring; and k is 0, 1, 2, 3, 4, or 5. In certain embodiments,k is 0. In certain embodiments, k is 1. In certain embodiments, k is 2.In certain embodiments, k is 3. In certain embodiments, k is 4. Incertain embodiments, k is 5. In certain embodiments, R₅ is hydrogen. Incertain embodiments, R₅ is optionally substituted, branched orunbranched C₁₋₆ alkyl. In certain embodiments, R₅ is unsubstitutedmethyl. In certain embodiments, R₅ is substituted methyl. In certainembodiments, R₅ is trifluoromethyl. In certain embodiments, R₅ isunsubstituted ethyl. In certain embodiments, R₅ is substituted ethyl. Incertain embodiments, R₅ is optionally substituted propyl. In certainembodiments, R₅ is substituted n-propyl. In certain embodiments, R₅ isunsubstituted n-propyl. In certain embodiments, R₅ is substitutediso-propyl. In certain embodiments, R₅ is unsubstituted iso-propyl. Incertain embodiments, R₅ is halogen. In certain embodiments, R₅ is I. Incertain embodiments, R₅ is Br. In certain embodiments, R₅ is Cl. Incertain embodiments, R₅ is F. In certain embodiments, R₅ is NO₂. Incertain embodiments, R₅ is —OH. In certain embodiments, R₅ is —CN.

In compounds of Formula (I), Y is N or CH. In certain embodiments, Y isN. In certain embodiments, Y is CH. In compounds of Formula (VI), Y is Nor CH. In certain embodiments, Y is N. In certain embodiments, Y is CH

In compounds of Formula (I) or (VI), linker X is a divalent linkermoiety. X may contain 0-4 carbon atoms or heteroatoms in the backbone ofX. X may be substituted or unsubstituted. X may be branched orunbranched. In certain embodiments, X is a bond. In certain embodiments,X is —C(═O)—. In certain embodiments, X is —O—. In certain embodiments,X is —S—. In certain embodiments, X is a substituted C₁₋₆ hydrocarbonchain. In certain embodiments, X is an unsubstituted C₁₋₆ hydrocarbonchain. In certain embodiments, X is —CH₂—. In certain embodiments, X is—(CH₂)₂—. In certain embodiments, X is —(CH₂)₃—In certain embodiments, Xis —(CH₂)₄—. In certain embodiments, X is —(CH₂)₅—In certainembodiments, X is —(CH₂)₆—In certain embodiments, X is an optionallysubstituted C₁₋₆ hydrocarbon chain, wherein one or more carbon units ofthe hydrocarbon chain is replaced with —O—, —S—, NR^(Xa)—,—NR^(Xa)C(═O)—, —C(═O)NR^(Xa)—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—,—NR^(Xa)C(═S)—, —C(═S)NR^(Xa)—, trans-CR^(L2b)═CR^(L2b)—,cis-CR^(Xb)═CR^(Xb)—, —C≡C—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(Xa)—, or—NR^(Xa)S(═O)₂—, wherein R^(Xa) is optionally substituted alkyl or anitrogen protecting group; and R^(Xb) is optionally substituted alkyl.In certain embodiments, X is —(C═O)(CH₂)₅—. In certain embodiments, X is—(C═O)(CH₂)₄—. In certain embodiments, X is —(C═O)(CH₂)₃—. In certainembodiments, X is —(C═O)(CH₂)₂—. In certain embodiments, X is—(C═O)CH₂—. In certain embodiments, X is —O(CH₂)₅—. In certainembodiments, X is —O(CH₂)₄—. In certain embodiments, X is —O(CH₂)₃—Incertain embodiments, X is —O(CH₂)₂—. In certain embodiments, X is—OCH₂—.

As defined generally above, R₂ is optionally substituted carbocyclic,optionally substituted heterocyclic, optionally substituted aryl, oroptionally substituted heteroaryl ring. In certain embodiments, R₂ isunsubstituted. In certain embodiments, R₂ is substituted with one, two,or three R^(B1) groups. In certain embodiments, R₂ is an optionallysubstituted monocyclic or bicyclic carbocyclic ring. In certainembodiments, R₂ is an optionally substituted monocyclic or bicyclicheterocyclic ring with 0-4 heteroatoms independently selected fromnitrogen, oxygen, and sulfur. In certain embodiments, R₂ is anoptionally substituted monocyclic or bicyclic heteroaryl ring.

In certain embodiments, R₂ is an optionally substituted monocyclichetero-ring with 1-4 oxygen. In certain embodiments, R₂ is an optionallysubstituted monocyclic ring with one oxygen. In certain embodiments, R₂is of the formula

In certain embodiments, p is 0 and R₂ is hydroxyl alkyl. In certainembodiments, p is 1. In certain embodiments, p is 2. In certainembodiments, p is 3. In certain embodiments, p is 4. In certainembodiments, q is 0 and R₂ is hydroxyl alkyl. In certain embodiments, qis 1. In certain embodiments, q is 2. In certain embodiments, q is 3. Incertain embodiments, q is 4. In certain embodiments, p is 1 and q is 1.In certain embodiments, p is 1 and q is 2. In certain embodiments, p is1 and q is 3. In certain embodiments, p is 1 and q is 4. In certainembodiments, p is 2 and q is 2. In certain embodiments, p is 2 and q is3. In certain embodiments, p is 2 and q is 4. In certain embodiments, pis 3 and q is 3. In certain embodiments, p is 3 and q is 4. In certainembodiments, p is 4 and q is 4. In certain embodiments, R₂ is of theformula

In certain embodiments, R₂ is an optionally substituted bicyclichetero-ring with 1-4 heteroatoms independently selected from nitrogenand oxygen. In certain embodiments, R₂ is an optionally substitutedbicyclic heterocyclic ring with one nitrogen and one oxygen. In certainembodiments, R₂ is of the formula

In certain embodiments, p is 1; q is 1; s is 1; and t is 1. In certainembodiments, p is 1; q is 1; s is 1; and t is 2. In certain embodiments,p is 1; q is 1; s is 1; and t is 3. In certain embodiments, p is 1; q is1; s is 2; and t is 2. In certain embodiments, p is 1; q is 1; s is 2; tis 3. In certain embodiments, p is 1; q is 1; s is 3; and t is 3. Incertain embodiments, p is 1; q is 1; s is 1; and t is 1. In certainembodiments, p is 1; q is 2; s is 1; t is 2. In certain embodiments, pis 1; q is 2; s is 1; and t is 3. In certain embodiments, p is 1; q is2; s is 2; and t is 2. In certain embodiments, p is 1; q is 2; s is 2;and t is 3. In certain embodiments, p is 1; q is 2; s is 3; and t is 3.In certain embodiments, p is 2; q is 2; s is 1; t is 1. In certainembodiments, p is 2; q is 2; s is 1; and t is 2. In certain embodiments,p is 2; q is 2; s is 1; and t is 3. In certain embodiments, p is 2; q is2; s is 2; and t is 2. In certain embodiments, p is 2; q is 2; s is 2;and t is 3. In certain embodiments, p is 2; q is 2; s is 3; and t is 3.In certain embodiments, R₂ is of one of the following structures:

-   In certain embodiments, R₂ is of the formula

In certain embodiments, R₁ is hydrogen. In certain embodiments, R₁ isoptionally substituted, branched or unbranched, C₁₋₆ alkyl. In certainembodiments, R₁ is substituted methyl. In certain embodiments, R₁ isunsubstituted methyl. In certain embodiments, R₁ is substituted ethyl.In certain embodiments, R₁ is unsubstituted ethyl. In certainembodiments, R₁ is optionally substituted propyl. In certainembodiments, R₁ is substituted n-propyl. In certain embodiments, R₁ isunsubstituted n-propyl. In certain embodiments, R₁ is substitutediso-propyl. In certain embodiments, R₁ is unsubstituted iso-propyl.

In certain embodiments, the compound of Formula (I) is of the Formula(II):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, R₄, X,Y, m, n, and j are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-a):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₄, X, Y,n, and j are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-b):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, X, Y, andn are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-c):

or pharmaceutically acceptable salts thereof, wherein R₂, X, Y, and nare as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-c1):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-c2):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-c3):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(II-c4):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, R₅, X,Y, m, n, and k are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-a):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₅, X, Y,n, and k are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-b):

or pharmaceutically acceptable salts thereof, wherein R₂, R₅, X, Y, n,and k are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-c):

or pharmaceutically acceptable salts thereof, wherein R₂, X, Y, and nare as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-c1):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-c2):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-c3):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(III-c4):

or pharmaceutically acceptable salts thereof, wherein R₂ and Y are asdescribed herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,m, and n are as described herein, and Z₁ is branched or unbranched,acyclic or cyclic C₁₋₆ alkyl. In certain embodiments, Z₁ is acyclic C₁₋₆alkyl. In certain embodiments, Z₁ is cyclic C₁₋₆ alkyl.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, X, Y, Z₁,and n are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a1):

or pharmaceutically acceptable salts thereof, wherein R₂, n, X, Y, andZ₁ are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a1-i):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a1-ii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a1-iii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-a1-iv):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, X, Y, andn are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b1):

or pharmaceutically acceptable salts thereof, wherein R₂, n, X, Y, andZ₁ are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b1-i):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b1-ii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b1-iii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(IV-b1-iv):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, and Z₁ areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, R₃, X, Y,e, f, m, and n are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, X, Y, e,f, and n are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a1):

or pharmaceutically acceptable salts thereof, wherein R₂, X, Y, n, e andf are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a1-i):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a1-ii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a1-iii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-a1-iv):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b):

or pharmaceutically acceptable salts thereof, wherein R₁, R₂, X, Y, n, eand f are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b1):

or pharmaceutically acceptable salts thereof, wherein R₂, X, Y, n, e andf are as described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b1-i):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b1-ii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b1-iii):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is of the Formula(V-b1-iv):

or pharmaceutically acceptable salts thereof, wherein R₂, Y, e and f areas described herein.

In certain embodiments, the compound of Formula (I) is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (I) is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of the invention is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of the invention is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (VI) is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, the compound of Formula (VI) is

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

Exemplary compounds of Formula (I) include but not limited to

Other exemplary compounds of the invention include but not limited to

Compounds of the invention may be crystalline. In certain embodiments,the compounds of the invention are monocrystalline. In certainembodiments, the compounds of the invention are polycrystalline.

Compounds of the invention may also have a relatively low aqueoussolubility (i.e., a solubility in water, optionally with one or morebuffers). For example, compounds of the invention may have an aqueoussolubility of less than about or equal to about 3 mg/mL, less than about1 mg/mL, less than about 0.3 mg/mL, less than about 0.1 mg/mL, less thanabout 0.03 mg/mL, less than about 0.01 mg/mL, less than about 1 μg/mL,less than about 0.1 μg/mL, less than about 0.01 μg/mL, less than about 1ng/mL, less than about 0.1 ng/mL, or less than about 0.01 ng/mL at 25°C. In some embodiments, the compounds of the invention have an aqueoussolubility of at least about 1 pg/mL, at least about 10 pg/mL, at leastabout 0.1 ng/mL, at least about 1 ng/mL, at least about 10 ng/mL, atleast about 0.1 μg/mL, at least about 1 μg/mL, at least about 3 μg/mL,at least about 0.01 mg/mL, at least about 0.03 mg/mL, at least about 0.1mg/mL, at least about 0.3 mg/mL, at least about 1.0 mg/mL, or at leastabout 3 mg/mL at 25° C. Combinations of the above-noted ranges arepossible (e.g., an aqueous solubility of at least about 10 pg/mL andless than about 1 mg/mL). Other ranges are also possible. The compoundsof the invention may have these or other ranges of aqueous solubilitiesat any point throughout the pH range (e.g., at about pH 7 or from pH 1to pH 14).

Compounds of the invention may be suitable for being processed intomucus-penetrating pharmaceutical compositions (e.g., particles orcrystals). In certain embodiments, the compounds of the invention aresuitable for milling (e.g., nano-milling). In certain embodiments, thecompounds of the invention are suitable for precipitation (e.g.,microprecipitation, nanoprecipitation, crystallization, or controlledcrystallization). In certain embodiments, the compounds of the inventionare suitable for emulsification. In certain embodiments, the compoundsof the invention are suitable for freeze-drying.

Synthetic Methods

In some embodiments, compounds described herein can be prepared usingmethods shown in Scheme 1:

Pharmaceutical Compositions, Kits, and Methods of Use

The present invention provides pharmaceutical compositions comprising acompound described herein, e.g., a compound of Formula (I) or a compoundof Formula (VI), or pharmaceutically acceptable salts thereof, asdescribed herein, and optionally a pharmaceutically acceptableexcipient. It will be understood by one of ordinary skill in the artthat the compounds described herein, or salts thereof, may be present ashydrates, solvates, or polymorphs. In certain embodiments, a providedcomposition comprises two or more compounds described herein. In certainembodiments, a compound described herein, or pharmaceutically acceptablesalts thereof, is provided in an effective amount in the pharmaceuticalcomposition. In certain embodiments, the effective amount is atherapeutically effective amount. In certain embodiments, the effectiveamount is an amount effective for treating a disease. In certainembodiments, the effective amount is an amount effective for treating agrowth factor-mediated disease. In certain embodiments, the effectiveamount is an amount effective for treating a VEGF-mediated disease. Incertain embodiments, the effective amount is a prophylacticallyeffective amount. In certain embodiments, the effective amount is anamount effective for treating a growth factor-mediated disease. Incertain embodiments, the effective amount is an amount effective toprevent a VEGF-mediated disease. In certain embodiments, the effectiveamount is an amount effective to treat an abnormalangiogenesis-associated disease such as atherosclerosis, hypertension,tumor growth, inflammation, rheumatoid arthritis, wet-form maculardegeneration, choroidal neovascularization, retinal neovascularization,and diabetic retinopathy. In certain embodiments, the effective amountis an amount effective to treat cancer. In certain embodiments, theeffective amount is an amount effective to treat macular degeneration.

Pharmaceutical compositions described herein can be prepared by anymethod known in the art of pharmacology. In general, such preparatorymethods include the steps of bringing a compound described herein (the“active ingredient”) into association with a carrier and/or one or moreother accessory ingredients, and then, if necessary and/or desirable,shaping and/or packaging the product into a desired single- ormulti-dose unit.

In certain embodiments, an effective amount of a compound foradministration one or more times a day to a 70 kg adult human maycomprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg,about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about1000 mg, about 10 mg to about 100 mg, or about 100 mg to about 1000 mgof a compound per unit dosage form.

Also encompassed by the present disclosure are kits (e.g.,pharmaceutical packs). The kits provided may comprise a providedpharmaceutical composition or compound and a container (e.g., a vial,ampule, bottle, syringe, and/or dispenser package, or other suitablecontainer). In some embodiments, provided kits may optionally furtherinclude a second container comprising a pharmaceutical excipient fordilution or suspension of a provided pharmaceutical composition orcompound. In some embodiments, a provided pharmaceutical composition orcompound provided in the container and the second container are combinedto form one unit dosage form. In some embodiments, a provided kitfurther includes instructions for use.

Also provided by the present invention are particles that may penetratemucus, pharmaceutical compositions thereof, kits, and methods of usingand preparing the particles, and pharmaceutical compositions thereof.The pharmaceutical compositions, kits, and methods may involve modifyingthe surface coatings of particles, such as particles of pharmaceuticalagents that have a low aqueous solubility. Such pharmaceuticalcompositions, kits, and methods can be used to achieve efficienttransport of particles comprising the inventive compounds through mucusbarriers in a subject.

In certain embodiments, the compounds, particles, pharmaceuticalcompositions, kits, and methods of the invention are useful forapplications in the eye, such as treating and/or preventing an oculardisease (e.g., macular degeneration, dry eye syndrome, uveitis, allergicconjunctivitis, glaucoma, and rosacea).

The particles (e.g., nanoparticles and microparticles) of the inventioncomprise a compound of the invention. The particles of the inventionalso include a surface-altering agent that modifies the surface of theparticles to reduce the adhesion of the particles to mucus and/or tofacilitate penetration of the particles through mucus.

The present invention also provides pharmaceutical compositionscomprising the inventive particles. In certain embodiments, thepharmaceutical compositions of the invention can be topicallyadministered to the eye of a subject. Topical pharmaceuticalcompositions are advantageous over pharmaceutical compositions that areadministered by injection or orally.

Particles

The present invention also provides pharmaceutical compositionscomprising a plurality of particles of the invention, which may bemucus-penetrating and may include a pharmaceutical agent (e.g., acompound of the invention). The inventive pharmaceutical compositionsmay be useful to deliver the pharmaceutical agent to the eye of asubject and to treat and/or prevent an ocular disease of the subject.

Without wishing to be bound by theory, it is believed that conventionalparticles (CPs, e.g., non-MPPs) are trapped in the mucus layer (e.g.,eye mucin) and are readily cleared from the subject. Thus, theconventional particles may be cleared before the drugs contained in theparticles can be transported to target tissue or site (e.g., bydiffusion or other mechanisms). In contrast, the particles of compoundsof the invention formulated as mucus-penetrating particles may avoidadhesion to secreted mucins, thereby prolonging particle retention andsustaining drug release.

In some embodiments, the particles of the invention have a core-shelltype configuration. The core may comprise the solid pharmaceutical agent(including but not limited to pharmaceutical agents having a relativelylow aqueous solubility), or may comprise a pharmaceutical agent and apolymeric carrier, a lipid, and/or a protein. The core may also comprisea gel or a liquid. The core may be coated with a coating or shellcomprising a surface-altering agent that facilitates mobility of theparticle in mucus. As described in more detail below, thesurface-altering agent may comprise a polymer (e.g., a synthetic or anatural polymer) having pendant hydroxyl groups on the backbone of thepolymer. The molecular weight and/or degree of hydrolysis of the polymermay be chosen to impart certain transport characteristics to theparticles, such as increased transport through mucus. In certainembodiments, the surface-altering agent may comprise a triblockcopolymer comprising a (hydrophilic block)-(hydrophobicblock)-(hydrophilic block) configuration. The molecular weights of eachone of the blocks may be chosen to impart certain transportcharacteristics to the particles, such as increased transport throughmucus. In some embodiments, at least one particle of the inventionincludes a core and a coating surrounding the core. A particle includinga core and a coating on the core is referred to as a “coated particle.”In certain embodiments, at least one particle of the invention includesa core but not a coating on the core. A particle including a core butnot a coating on the core is referred to as an “uncoated particle.”

In some embodiments, a substantial portion of the core is formed of oneor more solid pharmaceutical agents (e.g., a compound of the invention)that can lead to certain beneficial and/or therapeutic effects. The coremay be, for example, a nanocrystal (i.e., a nanocrystalline particle) ofa compound of Formula (I) or a compound of Formula (VI). In certainembodiments, the core includes a polymeric carrier with a compound ofFormula (I) or Formula (VI), and optionally with one or more otherpharmaceutical agents encapsulated or otherwise associated with thecore. In certain embodiments, the core includes a lipid, protein, gel,liquid, and/or another suitable material to be delivered to a subject.The core includes a surface to which one or more surface-altering agentscan be attached. In some embodiments, the core is surrounded by coating,which includes an inner surface and an outer surface. The coating may beformed, at least in part, of one or more surface-altering agents, suchas a polymer (e.g., a block copolymer and/or a polymer having pendanthydroxyl groups), which may associate with the surface of the core. Thesurface-altering agent may be associated with the core particle by, forexample, being covalently attached to the core particle, non-covalentlyattached to the core particle, adsorbed to the core, or attached to thecore through ionic interactions, hydrophobic and/or hydrophilicinteractions, electrostatic interactions, van der Waals interactions, orcombinations thereof. In some embodiments, the surface-altering agents,or portions thereof, are chosen to facilitate transport of the particlethrough or into a mucosal barrier (e.g., mucus or a mucosal membrane).In certain embodiments described herein, one or more surface-alteringagents are oriented in a particular configuration in the coating. Insome embodiments, in which a surface-altering agent is a triblockcopolymer, such as a triblock copolymer having a (hydrophilicblock)-(hydrophobic block)-(hydrophilic block) configuration, ahydrophobic block may be oriented towards the surface of the core, andhydrophilic blocks may be oriented away from the core surface (e.g.,towards the exterior of the particle). The hydrophilic blocks may havecharacteristics that facilitate transport of the particle through amucosal barrier, as described in more detail below.

It should be understood that components and configurations other thanthose described herein may be suitable for certain particles andpharmaceutical compositions, and that not all of the componentsdescribed are necessarily present in some embodiments.

In some embodiments, particles of the invention comprising compounds ofFormula (I) or Formula (VI), when introduced into a subject, mayinteract with one or more components in the subject such as mucus,cells, tissues, organs, particles, fluids (e.g., blood), microorganisms,and portions or combinations thereof. In some embodiments, the coatingof the inventive particle can be designed to include surface-alteringagents or other components with properties that allow favorableinteractions (e.g., transport, binding, and adsorption) with one or morematerials from the subject. For example, the coating may includesurface-altering agents or other components having a certainhydrophilicity, hydrophobicity, surface charge, functional group,specificity for binding, and/or density to facilitate or reduceparticular interactions in the subject. One example is choosing ahydrophilicity, hydrophobicity, surface charge, functional group,specificity for binding, and/or density of one or more surface-alteringagents to reduce the physical and/or chemical interactions between theparticle and mucus of the subject, so as to enhance the mobility of theparticle through mucus. Other examples are described in more detailbelow.

In some embodiments, once a particle is successfully transported intoand/or across a mucosal barrier (e.g., mucus or a mucosal membrane) in asubject, further interactions between the particle and the subject maytake place. In some embodiments, in which the core comprises apharmaceutical agent or compound of the invention, the conversion,breakdown, release, and/or transport of the pharmaceutical agent fromthe particle can lead to certain beneficial and/or therapeutic effectsin the subject. Therefore, the particles of the invention can be usedfor the treatment and/or prevention of certain diseases.

Examples for the use of the particles of the invention are providedbelow in the context of being suitable for administration to a mucosalbarrier (e.g., mucus or a mucosal membrane) in a subject. It should beappreciated that while many of the embodiments herein are described inthis context, and in the context of providing a benefit for diseasesthat involve transport of materials across a mucosal barrier, theinvention is not limited as such, and the particles, pharmaceuticalcompositions, and kits of the invention may be used to treat and/orprevent other diseases.

In some embodiments, the pharmaceutical compositions of the inventioncomprise MPPs that include a compound of the invention and optionally atleast one additional pharmaceutical agent, each of which is associatedwith polymer carriers via encapsulation or other processes. In otherembodiments, the pharmaceutical compositions of the invention compriseMPPs without any polymeric carriers or with minimal use of polymericcarriers. Polymer-based MPPs may have one or more inherent limitationsin some embodiments. In particular, in light of drug deliveryapplications, these limitations may include one or more of thefollowing. A) Low drug encapsulation efficiency and low drug loading:encapsulation of drugs into polymeric particles is often inefficient, asgenerally less than 10% of the total amount of drug used getsencapsulated into particles during manufacturing; additionally, drugloadings above 50% are rarely achieved. B) Convenience of usage:pharmaceutical compositions based on drug-loaded polymeric particles, ingeneral, typically need to be stored as dry powder to avoid prematuredrug release and thus require either point-of-use re-constitution or asophisticated dosing device. C) Biocompatibility: accumulation of slowlydegrading polymer carriers following repeated dosing and their toxicityover the long term present a major concern for polymeric drug carriers.D) Chemical and physical stability: polymer degradation may compromisestability of encapsulated drugs. In many encapsulation processes, thedrug undergoes a transition from a solution phase to a solid phase,which is not well-controlled in terms of physical form of the emergingsolid phase (i.e., amorphous vs. crystalline vs. crystallinepolymorphs); this is a concern for multiple aspects of pharmaceuticalcomposition performance, including physical and chemical stability andrelease kinetics. E) Manufacturing complexity: manufacturing, especiallyscalability, of drug-loaded polymeric MPPs is a fairly complex processthat may involve multiple steps and a considerable amount of toxicorganic solvents. Therefore, by avoiding or minimizing the need toencapsulate pharmaceutical agents into polymeric carriers, certainlimitations of polymeric MPPs with respect to drug loading, convenienceof usage, biocompatibility, stability, and/or complexity ofmanufacturing, may be addressed.

It should be appreciated, however, that in other embodiments,pharmaceutical agents may be associated with polymer carriers viaencapsulation or other processes. Thus, the description provided hereinis not limited in this respect. For instance, despite theabove-mentioned drawbacks of certain mucus-penetrating particlesincluding a polymeric carrier, in certain embodiments such particles maybe preferred. For example, it may be preferable to use polymer carriersfor controlled release purposes and/or for encapsulating certainpharmaceutical agents that are difficult to formulate into particles. Assuch, in some embodiments described herein, particles that include apolymer carrier are described.

In some embodiments, the pharmaceutical compositions of the inventioninvolve the use of poly(vinyl alcohols) (PVAs) to aid particle transportin mucus. The pharmaceutical compositions may involve makingmucus-penetrating particles by, for example, an emulsification processin the presence of specific PVAs. In certain embodiments, thepharmaceutical compositions and methods involve making mucus-penetratingparticles from pre-fabricated particles by non-covalent coating withspecific PVAs. In some embodiments, the pharmaceutical compositions andmethods involve making mucus-penetrating particles in the presence ofspecific PVAs without any polymeric carriers or with minimal use ofpolymeric carriers. It should be appreciated, however, that in otherembodiments, polymeric carriers can be used.

PVA is a water-soluble non-ionic synthetic polymer. Due to its surfaceactive properties, PVA is widely used in the food and drug industries asa stabilizing agent for emulsions and, in particular, to enableencapsulation of a wide variety of compounds by emulsificationtechniques. PVA has the “generally recognized as safe” (GRAS) statuswith the Food and Drug Administration (FDA), and has been used inauricular, intramuscular, intraocular, intravitreal, iontophoretic,ophthalmic, oral, topical, and transdermal drug products and/or drugdelivery systems. Mucus-penetrating particles can be prepared bytailoring the degree of hydrolysis and/or molecular weight of the PVA,which was previously unknown. This discovery significantly broadens thearsenal of techniques and ingredients applicable for manufacturing MPPs.

In other embodiments, the pharmaceutical compositions of the inventionand the methods of making the particles and pharmaceutical compositionsof the invention involve PVAs in conjunction with other polymers or donot involve PVAs at all. For example, PEG and/or PLURONICS® (poloxamers)may be included in the pharmaceutical compositions of the invention andmethods of making the particles and pharmaceutical compositions of theinvention, in addition to or in replace of PVAs. Other polymers, such asthose described herein, may also be used.

Core of the Particles

Particles of compounds of Formula (I) or (VI) of the inventionformulated to penetrate mucus include a core. The core of the inventiveparticles may be formed of any suitable material, such as an organicmaterial, inorganic material, polymer, lipid, protein, or combinationsthereof. In some embodiments, the core is a solid. The solid may be, forexample, a crystalline, semi-crystalline, or amorphous solid, such as acrystalline, semi-crystalline, or amorphous solid of a compound ofFormula (I) or (VI) of the invention), or a salt thereof. In certainembodiments, the core is a gel or liquid (e.g., an oil-in-water orwater-in-oil emulsion). In certain embodiment, the core is ananocrystal.

The compound of the invention may be present in the core in any suitableamount, (e.g., at least about 80 wt % and less than about 100 wt % ofthe core). Other ranges are also possible.

In certain embodiments, the core of the particles of the invention ishydrophobic. In certain embodiments, the core is substantiallyhydrophobic. In certain embodiments, the core is hydrophilic. In certainembodiments, the core is substantially hydrophilic.

In some embodiments, the core includes one or more organic materials,such as a synthetic polymer and/or natural polymer. Examples ofsynthetic polymers include non-degradable polymers (e.g.,polymethacrylate) and degradable polymers (e.g., polylactic acid andpolyglycolic acid), and copolymers thereof. Examples of natural polymersinclude hyaluronic acid, chitosan, and collagen. Other examples ofpolymers that may be suitable for portions of the core include thosesuitable for forming coatings on particles, as described herein. In somecases, the one or more polymers present in the core may be used toencapsulate or adsorb one or more pharmaceutical agents.

When a polymer is present in the core, the polymer may be present in thecore in any suitable amount, e.g., less than about 100 wt %, less thanabout 80 wt %, less than about 60 wt %, less than about 50 wt %, lessthan about 40 wt %, less than about 30 wt %, less than about 20 wt %,less than about 10 wt %, less than about 5 wt %, or less than about 1 wt%. In some cases, the polymer may be present in an amount of at leastabout 1 wt %, at least about 5 wt %, at least about 10 wt %, at leastabout 20 wt %, at least about 30 wt %, at least about 40 wt %, at leastabout 50 wt %, at least about 75 wt %, at least about 90 wt %, or atleast about 99 wt % in the core. Combinations of the above-referencedranges are also possible (e.g., present in an amount of at least about 1wt % and less than about 20 wt %). Other ranges are also possible. Insome embodiments, the core is substantially free of a polymericcomponent.

The core may have any suitable shape and/or size. For instance, the coremay be substantially spherical, non-spherical, oval, rod-shaped,pyramidal, cube-like, disk-shaped, wire-like, or irregularly shaped. Thecore may have a largest or smallest cross-sectional dimension of, forexample, less than about 10 μm, less than about 3 μm, less than about 1μm, less than about 500 nm, less than 400 nm, less than 300 nm, lessthan about 200 nm, less than about 100 nm, less than about 30 nm, orless than about 10 nm. In some cases, the core may have a largest orsmallest cross-sectional dimension of, for example, at least about 10nm, at least about 30 nm, at least about 100 nm, at least about 200 nm,at least about 300 nm, at least about 400 nm, at least about 500 nm, atleast about 1 μm, or at least about 3 μm. Combinations of theabove-referenced ranges are also possible (e.g., a largest or smallestcross-sectional dimension of at least about 30 nm and less than about500 nm). Other ranges are also possible. In some embodiments, the sizesof the cores formed by a process described herein have a Gaussian-typedistribution. Unless indicated otherwise, the measurements of theparticle sizes or core sizes refer to the smallest cross-sectionaldimension.

Techniques to determine sizes (e.g., smallest or largest cross-sectionaldimensions) of particles are known in the art. Examples of suitabletechniques include dynamic light scattering (DLS), transmission electronmicroscopy, scanning electron microscopy, electroresistance counting andlaser diffraction. Although many methods for determining sizes ofparticles are known, the sizes described herein (e.g., average particlesizes and thicknesses) refer to ones measured by DLS.

Coating of the Particles

A particle of the invention may include a coating. An inventive particlecomprising a compound of Formula (I) or (VI) including a coating may bereferred to as a coated particle of the invention. An inventive particlenot including a coating may be referred to as an uncoated particle ofthe invention. In some embodiments, the coating is formed of one or moresurface-altering agents or other molecules disposed on the surface ofthe core. The particular chemical makeup and/or components of thecoating and surface-altering agent(s) can be chosen so as to impartcertain functionality to the particles, such as enhanced transportthrough mucosal barriers.

It should be understood that a coating which surrounds a core need notcompletely surround the core, although such embodiments may be possible.For example, the coating may surround at least about 10%, at least about30%, at least about 50%, at least about 70%, at least about 90%, or atleast about 99% of the surface area of a core. In some cases, thecoating substantially surrounds a core. In other cases, the coatingcompletely surrounds a core. In other embodiments, a coating surroundsless than about 100%, less than about 90%, less than about 70%, or lessthan about 50% of the surface area of a core. Combinations of theabove-referenced ranges are also possible (e.g., surrounding at least70% and less than 100% of the surface area of a core).

The material of the coating may be distributed evenly across a surfaceof the core in some cases, and unevenly in other cases. For example, thecoating may include portions (e.g., holes) that do not include anymaterial. If desired, the coating may be designed to allow penetrationand/or transport of certain molecules and components into or out of thecoating, but may prevent penetration and/or transport of other moleculesand components into or out of the coating. The ability of certainmolecules to penetrate and/or be transported into and/or across acoating may depend on, for example, the packing density of thesurface-altering agents forming the coating and the chemical andphysical properties of the components forming the coating. As describedherein, the coating may include one layer of material (i.e., amonolayer) or multilayers of materials. A single type or multiple typesof surface-altering agent may be present.

The coating of particles of the invention can have any suitablethickness. For example, the coating may have an average thickness of atleast about 1 nm, at least about 3 nm, at least about 10 nm, at leastabout 30 nm, at least about 100 nm, at least about 300 nm, at leastabout 1 μm, or at least about 3 μm. In some cases, the average thicknessof the coating is less than about 3 μm, less than about 1 μm, less thanabout 300 nm, less than about 100 nm, less than about 30 nm, less thanabout 10 nm, or less than about 3 nm. Combinations of theabove-referenced ranges are also possible (e.g., an average thickness ofat least about 1 nm and less than about 100 nm). Other ranges are alsopossible. For particles having multiple coatings, each coating may haveone of the thicknesses described herein.

The pharmaceutical compositions of the invention may allow for thecoating of the particles of the invention with hydrophilicsurface-altering moieties without requiring covalent association of thesurface-altering moieties to the surface of the core. In someembodiments, the core having a hydrophobic surface is coated with apolymer described herein, thereby causing a plurality ofsurface-altering moieties to be on the surface of the core withoutsubstantially altering the characteristics of the core itself. Forexample, the surface altering agent may be present on (e.g., adsorbedto) the outer surface of the core. In other embodiments, asurface-altering agent is covalently linked to the core.

In certain embodiments in which the surface-altering agent is adsorbedonto a surface of the core, the surface-altering agent may be inequilibrium with other molecules of the surface-altering agent insolution, optionally with other components (e.g., in a pharmaceuticalcomposition). In some cases, the adsorbed surface-altering agent may bepresent on the surface of the core at a density described herein. Thedensity may be an average density as the surface altering agent is inequilibrium with other components in solution.

The coating and/or surface-altering agent of the particles of theinvention may comprise any suitable material, such as a hydrophobicmaterial, a hydrophilic material, and/or an amphiphilic material. Insome embodiments, the coating includes a polymer. In certainembodiments, the polymer is a synthetic polymer (i.e., a polymer notproduced in nature). In other embodiments, the polymer is a naturalpolymer (e.g., a protein, polysaccharide, or rubber). In certainembodiments, the polymer is a surface active polymer. In certainembodiments, the polymer is a non-ionic polymer. In certain embodiments,the polymer is a linear synthetic non-ionic polymer. In certainembodiments, the polymer is a non-ionic block copolymer. The polymer maybe a copolymer. In certain embodiments, one repeat unit of the copolymeris relatively hydrophobic and another repeat unit of the copolymer isrelatively hydrophilic. The copolymer may be, for example, a diblock,triblock, alternating, or random copolymer. The polymer may be chargedor uncharged.

In some embodiments, the coating of the particles of the inventioncomprises a synthetic polymer having pendant hydroxyl groups on thebackbone of the polymer. Examples of the synthetic polymer are asdescribed herein. Without wishing to be bound by theory, a particleincluding a coating comprising a synthetic polymer having pendanthydroxyl groups on the backbone of the polymer may have reducedmucoadhesion as compared to a control particle due to, at least in part,the display of a plurality of hydroxyl groups on the particle surface.One possible mechanism for the reduced mucoadhesion is that the hydroxylgroups alter the microenvironment of the particle, for example, byordering water and other molecules in the particle/mucus environment. Anadditional or alternative possible mechanism is that the hydroxyl groupsshield the adhesive domains of the mucin fibers, thereby reducingparticle adhesion and speeding up particle transport.

Moreover, the ability of a particle coated with a synthetic polymerhaving pendant hydroxyl groups on the backbone of the polymer to bemucus penetrating may also depend, at least in part, on the degree ofhydrolysis of the polymer. In some embodiments, the hydrophobic portionsof the polymer (e.g., portions of the polymer that are not hydrolyzed)allow the polymer to be adhered to the surface of the core (e.g., in thecase that the surface of the core is hydrophobic), thus allowing for astrong association between the core and polymer. A synthetic polymerhaving pendant hydroxyl groups on the backbone of the polymer may haveany suitable degree of hydrolysis (and, therefore, varying amounts ofhydroxyl groups). The appropriate level of hydrolysis may depend onadditional factors, such as the molecular weight of the polymer, thepharmaceutical composition of the core, and the hydrophobicity of thecore. In some embodiments, the synthetic polymer is at least about 30%hydrolyzed, at least about 40% hydrolyzed, at least about 50%hydrolyzed, at least about 60% hydrolyzed, at least about 70%hydrolyzed, at least about 80% hydrolyzed, at least about 90%hydrolyzed, or at least about 95% hydrolyzed. In some embodiments, thesynthetic polymer is less than about 100% hydrolyzed, less than about95% hydrolyzed, less than about 90% hydrolyzed, less than about 80%hydrolyzed, less than about 70% hydrolyzed, or less than about 60%hydrolyzed. Combinations of the above-mentioned ranges are also possible(e.g., a synthetic polymer that is at least about 80% and less thanabout 95% hydrolyzed). Other ranges are also possible.

The molecular weight of the synthetic polymer described herein (e.g.,one having pendant hydroxyl groups on the backbone of the polymer) maybe selected so as to reduce the mucoadhesion of a core and to ensuresufficient association of the polymer with the core. In certainembodiments, the molecular weight of the synthetic polymer is at leastabout 1 kDa, at least about 2 kDa, at least about 5 kDa, at least about8 kDa, at least about 9 kDa, at least about 10 kDa, at least about 12kDa, at least about 15 kDa at least about 20 kDa, at least about 25 kDa,at least about 30 kDa, at least about 40 kDa, at least about 50 kDa, atleast about 60 kDa, at least about 70 kDa, at least about 80 kDa, atleast about 90 kDa, at least about 100 kDa at least about 110 kDa, atleast about 120 kDa, at least about 130 kDa, at least about 140 kDa, atleast about 150 kDa, at least about 200 kDa, at least about 500 kDa, orat least about 1000 kDa. In some embodiments, the molecular weight ofthe synthetic polymer is less than about 1000 kDa, less than about 500kDa, less than about 200 kDa, less than about, less than about 150 kDa,less than about 130 kDa, less than about 120 kDa, less than about 100kDa, less than about 85 kDa, less than about 70 kDa, less than about 65kDa, less than about 60 kDa, less than about 50 kDa, or less than about40 kDa, less than about 30 kDa, less than about 20 kDa, less than about15 kDa, or less than about 10 kDa. Combinations of the above-mentionedranges are also possible (e.g., a molecular weight of at least about 10kDa and less than about 30 kDa). The above-mentioned molecular weightranges can also be combined with the above-mentioned hydrolysis rangesto form suitable polymers.

In some embodiments, the synthetic polymer described herein is orcomprises PVA. In some embodiments, the synthetic polymer describedherein is or comprises partially hydrolyzed PVA. Partially hydrolyzedPVA includes two types of repeating units: vinyl alcohol units andresidual vinyl acetate units. The vinyl alcohol units are relativelyhydrophilic, and the vinyl acetate units are relatively hydrophobic. Insome instances, the sequence distribution of vinyl alcohol units andvinyl acetate units is blocky. For example, a series of vinyl alcoholunits may be followed by a series of vinyl acetate units, and followedby more vinyl alcohol units to form a polymer having a mixedblock-copolymer type arrangement, with units distributed in a blockymanner. In certain embodiments, the repeat units form a copolymer, e.g.,a diblock, triblock, alternating, or random copolymer. Polymers otherthan PVA may also have these configurations of hydrophilic units andhydrophobic units.

In some embodiments, the hydrophilic units of the synthetic polymerdescribed herein are substantially present at the outer surface of theparticles of the invention. For example, the hydrophilic units may forma majority of the outer surface of the coating and may help stabilizethe particles in an aqueous solution containing the particles. Thehydrophobic units may be substantially present in the interior of thecoating and/or at the surface of the core, e.g., to facilitateattachment of the coating to the core.

The molar fraction of the relatively hydrophilic units and therelatively hydrophobic units of the synthetic polymer described hereinmay be selected so as to reduce the mucoadhesion of a core and to ensuresufficient association of the polymer with the core, respectively. Asdescribed herein, the molar fraction of the hydrophobic units of thepolymer may be chosen such that adequate association of the polymer withthe core occurs, thereby increasing the likelihood that the polymerremains adhered to the core. The molar fraction of the relativelyhydrophilic units to the relatively hydrophobic units of the syntheticpolymer may be, for example, at least 0.5:1, at least 1:1, at least 2:1,at least 3:1, at least 5:1, at least 10:1, at least 20:1, at least 30:1,at least 50:1, or at least 100:1. In some embodiments, the molarfraction of the relatively hydrophilic units to the relativelyhydrophobic units of the synthetic polymer may be, for example, lessthan 100:1, less than 50:1, less than 30:1, less than 20:1, less than10:1, less than 5:1, less than 3:1, less than 2:1, or less than 1:1.Combinations of the above-referenced ranges are also possible (e.g., aratio of at least 1:1 and less than 50:1). Other ranges are alsopossible.

The molecular weight of the PVA polymer may also be tailored to increasethe effectiveness of the polymer to render particles mucus penetrating.Examples of PVA polymers having various molecular weights and degree ofhydrolysis are shown in Table 1.

TABLE 1 Molecular weight (MW) and degree of hydrolysis of variouspoly(vinyl alcohols) (PVAs).^(a) Hydrolysis PVA MW (kDa) degree (%) 2K75 2 75-79 9K80  9-10 80 13K87 13-23 87-89 13K98 13-23 98 31K87 31-5087-89 31K98 31-50 98-99 57K86 57-60 86-89 85K87  85-124 87-89 85K99 85-124   99+ 95K95  95 95 105K80 104 80 130K87 130 87-89 ^(a)The valuesof the molecular weight and hydrolysis degree of the PVAs were providedby the manufacturers of the PVAs.

In certain embodiments, the synthetic polymer is represented by theformula:

wherein:

u is an integer between 0 and 22730, inclusive; and

v is an integer between 0 and 11630, inclusive.

In some embodiments, the particles of the invention include a coatingcomprising a block copolymer having a relatively hydrophilic block and arelatively hydrophobic block. In some cases, the hydrophilic blocks maybe substantially present at the outer surface of the particle. Forexample, the hydrophilic blocks may form a majority of the outer surfaceof the coating and may help stabilize the particle in an aqueoussolution containing the particle. The hydrophobic block may besubstantially present in the interior of the coating and/or at thesurface of the core, e.g., to facilitate attachment of the coating tothe core. In some embodiments, the coating comprises a surface-alteringagent including a triblock copolymer, wherein the triblock copolymercomprises a (hydrophilic block)-(hydrophobic block)-(hydrophilic block)configuration. Diblock copolymers having a (hydrophilicblock)-(hydrophobic block) configuration are also possible. Combinationsof block copolymers with other polymers suitable for use as coatings arealso possible. Non-linear block configurations are also possible such asin comb, brush, or star copolymers. In some embodiments, the relativelyhydrophilic block includes a synthetic polymer having pendant hydroxylgroups on the backbone of the polymer (e.g., PVA).

The molecular weight of the hydrophilic blocks and the hydrophobicblocks of the block copolymers described herein may be selected so as toreduce the mucoadhesion of a core and to ensure sufficient associationof the block copolymer with the core, respectively. The molecular weightof the hydrophobic block of the block copolymer may be chosen such thatadequate association of the block copolymer with the core occurs,thereby increasing the likelihood that the block copolymer remainsadhered to the core.

In certain embodiments, the molecular weight of each block of orcombined blocks of the (one or more) relatively hydrophobic blocks of ablock copolymer is at least about 0.5 kDa, at least about 1 kDa, atleast about 1.8 kDa, at least about 2 kDa, at least about 3 kDa, atleast about 4 kDa, at least about 5 kDa, at least about 6 kDa, at leastabout 10 kDa, at least about 12 kDa, at least about 15 kDa, at leastabout 20 kDa, or at least about 50 kDa, at least about 60 kDa, at leastabout 70 kDa, at least about 80 kDa, at least about 90 kDa, at leastabout 100 kDa at least about 110 kDa, at least about 120 kDa, at leastabout 130 kDa, at least about 140 kDa, at least about 150 kDa, at leastabout 200 kDa, at least about 500 kDa, or at least about 1000 kDa. Insome embodiments, the molecular weight of each block of or combinedblocks of the (one or more) relatively hydrophobic blocks is less thanabout 1000 kDa, less than about 500 kDa, less than about 200 kDa, lessthan about 150 kDa, less than about 140 kDa, less than about 130 kDa,less than about 120 kDa, less than about 110 kDa, less than about 100kDa, less than about 90 kDa, less than about 80 kDa, less than about 50kDa, less than about 20 kDa, less than about 15 kDa, less than about 13kDa, less than about 12 kDa, less than about 10 kDa, less than about 8kDa, or less than about 6 kDa. Combinations of the above-mentionedranges are also possible (e.g., at least about 3 kDa and less than about15 kDa). Other ranges are also possible.

In some embodiments, the combined relatively hydrophilic blocks (e.g.,two hydrophilic blocks of a triblock copolymer) of a block copolymer(e.g., a triblock copolymer) constitute at least about 10 wt %, at leastabout 20 wt %, at least about 30 wt %, at least about 40 wt %, at leastabout 50 wt %, at least about 60 wt %, or at least about 70 wt % of theblock copolymer. In some embodiments, the combined (one or more)relatively hydrophilic blocks of a block copolymer constitute less thanabout 90 wt %, less than about 80 wt %, less than about 60 wt %, lessthan about 50 wt %, or less than about 40 wt % of the block copolymer.Combinations of the above-referenced ranges are also possible (e.g., atleast about 30 wt % and less than about 70 wt %). Other ranges are alsopossible.

In some embodiments, the molecular weight of each block of or combinedblocks of the (one or more) relatively hydrophilic blocks of the blockcopolymer may be at least about 0.5 kDa, at least about 1 kDa, at leastabout 1.8 kDa, at least about 2 kDa, at least about 3 kDa, at leastabout 4 kDa, at least about 5 kDa, at least about 6 kDa, at least about10 kDa, at least about 12 kDa, at least about 15 kDa, at least about 20kDa, or at least about 50 kDa, at least about 60 kDa, at least about 70kDa, at least about 80 kDa, at least about 90 kDa, at least about 100kDa at least about 110 kDa, at least about 120 kDa, at least about 130kDa, at least about 140 kDa, at least about 150 kDa, at least about 200kDa, at least about 500 kDa, or at least about 1000 kDa. In certainembodiments, the molecular weight of each block of or combined blocks ofthe (one or more) relatively hydrophilic blocks is less than about 1000kDa, less than about 500 kDa, less than about 200 kDa, less than about150 kDa, less than about 140 kDa, less than about 130 kDa, less thanabout 120 kDa, less than about 110 kDa, less than about 100 kDa, lessthan about 90 kDa, less than about 80 kDa, less than about 50 kDa, lessthan about 20 kDa, less than about 15 kDa, less than about 13 kDa, lessthan about 12 kDa, less than about 10 kDa, less than about 8 kDa, lessthan about 6 kDa, less than about 5 kDa, less than about 3 kDa, lessthan about 2 kDa, or less than about 1 kDa. Combinations of theabove-mentioned ranges are also possible (e.g., at least about 0.5 kDaand less than about 3 kDa). Other ranges are also possible. Inembodiments in which two hydrophilic blocks flank a hydrophobic block,the molecular weights of the two hydrophilic blocks may be substantiallythe same or different.

In certain embodiments, the polymer of the surface-altering agentincludes a polyether portion. In certain embodiments, the polymerincludes a polyalkylether portion. In certain embodiments, the polymerincludes polyethylene glycol (PEG) tails. In certain embodiments, thepolymer includes a polypropylene glycol as the central portion. Incertain embodiments, the polymer includes polybutylene glycol as thecentral portion. In certain embodiments, the polymer includespolypentylene glycol as the central portion. In certain embodiments, thepolymer includes polyhexylene glycol as the central portion. In certainembodiments, the polymer is a triblock copolymer of one of the polymersdescribed herein. In some embodiments, a diblock or triblock copolymercomprises a synthetic polymer having pendant hydroxyl groups on thebackbone of the polymer (e.g., PVA) as one or more of the blocks (withvarying degrees of hydrolysis and varying molecular weights as describedherein). The synthetic polymer blocks may form the central portion orend portions of the block copolymer.

In certain embodiments, the polymer is a triblock copolymer of apolyalkyl ether (e.g., polyethylene glycol, polypropylene glycol) andanother polymer (e.g., a synthetic polymer having pendant hydroxylgroups on the backbone of the polymer (e.g., PVA). In certainembodiments, the polymer is a triblock copolymer of a polyalkyl etherand another polyalkyl ether. In certain embodiments, the polymer is atriblock copolymer of polyethylene glycol and another polyalkyl ether.In certain embodiments, the polymer is a triblock copolymer ofpolypropylene glycol and another polyalkyl ether. In certainembodiments, the polymer is a triblock copolymer with at least one unitof polyalkyl ether. In certain embodiments, the polymer is a triblockcopolymer of two different polyalkyl ethers. In certain embodiments, thepolymer is a triblock copolymer including a polyethylene glycol unit. Incertain embodiments, the polymer is a triblock copolymer including apolypropylene glycol unit. In certain embodiments, the polymer is atriblock copolymer of a more hydrophobic unit flanked by two morehydrophilic units. In certain embodiments, the hydrophilic units are thesame type of polymer. In some embodiments, the hydrophilic units includea synthetic polymer having pendant hydroxyl groups on the backbone ofthe polymer (e.g., PVA). In certain embodiments, the polymer includes apolypropylene glycol unit flanked by two more hydrophilic units. Incertain embodiments, the polymer includes two polyethylene glycol unitsflanking a more hydrophobic unit. In certain embodiments, the polymer isa triblock copolymer with a polypropylene glycol unit flanked by twopolyethylene glycol units. The molecular weights of the two blocksflanking the central block may be substantially the same or different.

In certain embodiments, the polymer is of the formula:

wherein each instance of p is independently an integer between 2 and1140, inclusive; and q is an integer between 2 and 1730, inclusive. Incertain embodiments, each instance of p is independently an integerbetween 10 and 170, inclusive. In certain embodiments, q is an integerbetween 5 and 70 inclusive. In certain embodiments, each instance of pis independently at least 2 times of q, 3 times of q, or 4 times of q.

In certain embodiments, the surface-altering agent comprises a(poly(ethylene glycol))-(poly(propylene oxide))-(poly(ethylene glycol))triblock copolymer (PEG-PPO-PEG triblock copolymer), present in thecoating alone or in combination with another polymer such as a syntheticpolymer having pendant hydroxyl groups on the backbone of the polymer(e.g., PVA). The molecular weights of the PEG and PPO segments of thePEG-PPO-PEG triblock copolymer may be selected so as to reduce themucoadhesion of the particles, as described herein. Without wishing tobe bound by any theory, the particles of the invention having a coatingcomprising a PEG-PPO-PEG triblock copolymer may have reducedmucoadhesion as compared to control particles due to, at least in part,the PEG segments on the surface of the particles of the invention. ThePPO segment may be adhered to the surface of the core (e.g., in the caseof the surface of the core being hydrophobic), thus allowing for astrong association between the core and the triblock copolymer. In someembodiments, the PEG-PPO-PEG triblock copolymer is associated with thecore through non-covalent interactions. For purposes of comparison, thecontrol particle may be, for example, a carboxylate-modified polystyreneparticle of similar size as the particle of the invention.

In certain embodiments, the surface-altering agent includes a polymercomprising a poloxamer, having the trade name PLURONIC®. PLURONIC®polymers that may be useful in the embodiments described herein include,but are not limited to, F127, F38, F108, F68, F77, F87, F88, F98, L101,L121, L31, L35, L43, L44, L61, L62, L64, L81, L92, N3, P103, P104, P105,P123, P65, P84, and P85. Examples of molecular weights of certainPLURONIC® polymers are shown in Table 2.

TABLE 2 Molecular weight (MW) of PLURONIC ® polymers MW of MW of Averagethe PPO the PEG MW portion portion PLURONIC ® (Da) (Da) PEG wt % (Da)F127 12000  3600 70 8400 L44 2000 1200 40 800 L81 2667 2400 10 267 L1013333 3000 10 333 P65 3600 1800 50 1800 L121 4000 3600 10 400 P103 42863000 30 1286 F38 4500  900 80 3600 P123 5143 3600 30 1543 P105 6000 300050 3000 F87 8000 2400 70 5600 F68 9000 1800 80 7200 P123 5750 4030 301730

Although other ranges may be possible, in some embodiments, thehydrophobic block of the PEG-PPO-PEG triblock copolymer has one of themolecular weights described above (e.g., at least about 3 kDa and lessthan about 15 kDa), and the combined hydrophilic blocks have a weightpercentage with respect to the polymer in one of the ranges describedabove (e.g., at least about 15 wt %, at least about 20 wt %, at leastabout 25 wt %, or at least about 30 wt %, and less than about 80 wt %).Certain PLURONIC® polymers that fall within these criteria include, forexample, F127 (poloxamer 407), F108 (poloxamer 338), P105, and P103. Incertain embodiments, the particles of the invention including PLURONIC®polymers that fall within these criteria are more mucus penetrating thanparticles including PLURONIC® polymers that did not fall within thesecriteria. Materials that do not render the particles mucus penetratingalso include certain polymers such as polyvinylpyrrolidones(PVP/KOLLIDON), polyvinyl alcohol-polyethylene glycol graft-copolymer(KOLLICOAT IR), and hydroxypropyl methylcellulose (METHOCEL); oligomerssuch as TWEEN 20, TWEEN 80, solutol HS 15, TRITON X100, tyloxapol, andCREMOPHOR RH 40; and small molecules such as SPAN 20, SPAN 80, octylglucoside, cetytrimethylammonium bromide (CTAB), and sodium dodecylsulfate (SDS).

Although much of the description herein may involve coatings comprisinga (hydrophilic block)-(hydrophobic block)-(hydrophilic block)configuration (e.g., a PEG-PPO-PEG triblock copolymer) or coatingscomprising a synthetic polymer having pendant hydroxyl groups, it shouldbe appreciated that the coatings are not limited to these configurationsand materials and that other configurations and materials are possible.

Furthermore, although many of the embodiments described herein involve asingle coating, in other embodiments, a particle may include more thanone coating (e.g., at least two, three, four, five, or more coatings),and each coating need not be formed of or comprise a mucus penetratingmaterial. In some embodiments, an intermediate coating (i.e., a coatingbetween the core surface and an outer coating) may include a polymerthat facilitates attachment of an outer coating to the core surface. Insome embodiments, an outer coating of a particle includes a polymercomprising a material that facilitates the transport of the particlethrough mucus.

The coating (e.g., an inner coating, intermediate coating, and/or outercoating) of the particles of the invention may include any suitablepolymer. In some embodiments, the polymer of the coating isbiocompatible and/or biodegradable. In some embodiments, the polymer ofthe coating comprises more than one type of polymer (e.g., at least two,three, four, five, or more types of polymers). In some embodiments, thepolymer of the coating is a random copolymer or a block copolymer (e.g.,a diblock or triblock copolymer) as described herein.

Non-limiting examples of suitable polymers of the coating may includepolyamines, polyethers, polyamides, polyesters, polycarbamates,polyureas, polycarbonates, polystyrenes, polyimides, polysulfones,polyurethanes, polyacetylenes, polyethylenes, polyethyeneimines,polyisocyanates, polyacrylates, polymethacrylates, polyacrylonitriles,and polyarylates. Non-limiting examples of specific polymers includepoly(caprolactone) (PCL), ethylene vinyl acetate polymer (EVA),poly(lactic acid) (PLA), poly(L-lactic acid) (PLLA), poly(glycolic acid)(PGA), poly(lactic acid-co-glycolic acid) (PLGA), poly(L-lacticacid-co-glycolic acid) (PLLGA), poly(D,L-lactide) (PDLA),poly(L-lactide) (PLLA), poly(D,L-lactide-co-caprolactone),poly(D,L-lactide-co-caprolactone-co-glycolide),poly(D,L-lactide-co-PEO-co-D,L-lactide),poly(D,L-lactide-co-PPO-co-D,L-lactide), polyalkyl cyanoacrylate,polyurethane, poly-L-lysine (PLL), hydroxypropyl methacrylate (HPMA),poly(ethylene glycol), poly-L-glutamic acid, poly(hydroxy acids),polyanhydrides, polyorthoesters, poly(ester amides), polyamides,poly(ester ethers), polycarbonates, polyalkylenes such as polyethyleneand polypropylene, polyalkylene glycols such as poly(ethylene glycol)(PEG), polyalkylene terephthalates such as poly(ethylene terephthalate),polyvinyl alcohols (PVA), polyvinyl ethers, polyvinyl esters such aspoly(vinyl acetate), polyvinyl halides such as poly(vinyl chloride)(PVC), polyvinylpyrrolidone, polysiloxanes, polystyrene (PS),polyurethanes, derivatized celluloses such as alkyl celluloses,hydroxyalkyl celluloses, cellulose ethers, cellulose esters, nitrocelluloses, hydroxypropylcellulose, carboxymethylcellulose, polymers ofacrylic acids, such as poly(methyl(meth)acrylate) (PMMA),poly(ethyl(meth)acrylate), poly(butyl(meth)acrylate),poly(isobutyl(meth)acrylate), poly(hexyl(meth)acrylate),poly(isodecyl(meth)acrylate), poly(lauryl(meth)acrylate),poly(phenyl(meth)acrylate), poly(methyl acrylate), poly(isopropylacrylate), poly(isobutyl acrylate), poly(octadecyl acrylate) (jointlyreferred to herein as “polyacrylic acids”), and copolymers and mixturesthereof, polydioxanone and its copolymers, polyhydroxyalkanoates,polypropylene fumarate), polyoxymethylene, poloxamers,poly(ortho)esters, poly(butyric acid), poly(valeric acid),poly(lactide-co-caprolactone), and trimethylene carbonate.

The molecular weight of the polymer of the coating may vary. In someembodiments, the molecular weight of the polymer of the coating is atleast about 0.5 kDa, at least about 1 kDa, at least about 1.8 kDa, atleast about 2 kDa, at least about 3 kDa, at least about 4 kDa, at leastabout 5 kDa, at least about 6 kDa, at least about 8 kDa, at least about10 kDa, at least about 12 kDa, at least about 15 kDa, at least about 20kDa, at least about 30 kDa, at least about 40 kDa, or at least about 50kDa. In some embodiments, the molecular weight of the polymer of thecoating is less than about 50 kDa, less than about 40 kDa, less thanabout 30 kDa, less than about 20 kDa, less than about 12 kDa, less thanabout 10 kDa, less than about 8 kDa, less than about 6 kDa, less thanabout 5 kDa, or less than about 4 kDa. Combinations of theabove-referenced ranges are possible (e.g., a molecular weight of atleast about 2 kDa and less than about 15 kDa). Other ranges are alsopossible. The molecular weight of the polymer of the coating may bedetermined using any known technique such as light-scattering and gelpermeation chromatography. Other methods are known in the art.

In certain embodiments, the molecular weight of the hydrophobic block ofthe triblock copolymer of the (hydrophilic block)-(hydrophobicblock)-(hydrophilic block) configuration is at least about 2 kDa, andthe two hydrophilic blocks constitute at least about 15 wt % of thetriblock copolymer.

In certain embodiments, the polymer of the coating is biocompatible. Incertain embodiments, the polymer of the coating is biodegradable. Allbiocompatible polymers and biodegrade polymers are contemplated to bewithin the scope of the invention. In certain embodiments, a polymerdegrades in vivo within a period that is acceptable for the desiredapplication. For example, in an in vivo therapy, the polymer degrades ina period less than about five years, about one year, about six months,about three months, about one month, about two weeks, about one week,about three days, about one day, about six hours, or about one hour uponexposure to a physiological environment with a pH between about 6 andabout 8 having a temperature of between about 25 and about 37° C. Insome embodiments, the polymer of the coating degrades in a period ofbetween about one hour and several weeks, depending on the desiredapplication.

Although the particles of the invention, and the coating thereof, mayeach include polymers, in some embodiments, the particles of theinvention comprise a hydrophobic material that is not a polymer orpharmaceutical agent. Non-limiting examples of non-polymeric hydrophobicmaterials include, for example, metals, waxes, and organic materials(e.g., organic silanes and perfluorinated or fluorinated organicmaterials).

Particles with Reduced Mucoadhesion

Coated particles of the invention may have reduced mucoadhesiveness. Amaterial in need of increased diffusivity through mucus may behydrophobic, may include many hydrogen bond donors or acceptors, and/ormay be highly charged. In some cases, the material may include acrystalline or amorphous solid material. The material, which may serveas a core, may be coated with a suitable polymer described herein,thereby forming a particle with a plurality of surface-altering moietieson the surface, resulting in reduced mucoadhesion. Particles of theinvention as having reduced mucoadhesion may alternatively becharacterized as having increased transport through mucus, being mobilein mucus, or mucus-penetrating (i.e., mucus-penetrating particles),meaning that the particles are transported through mucus faster than anegative control particle. The negative control particle may be aparticle that is known to be mucoadhesive, e.g., an unmodified particleor core that is not coated with a coating described herein, such as a200 nm carboxylated polystyrene particle.

Coated particles of the invention may be adapted for delivery (e.g.,ocular delivery) to mucus or a mucosal surface of a subject. Theparticles with surface-altering moieties may be delivered to the mucosalsurface of a subject, may pass through the mucosal barrier in thesubject, and/or prolonged retention and/or increased uniformdistribution of the particles at mucosal surfaces, e.g., due to reducedmucoadhesion.

Furthermore, in some embodiments, the coated particles of the inventionhaving reduced mucoadhesion facilitate better distribution of theparticles at the surface of a tissue of a subject and/or have aprolonged presence at the surface of the tissue, compared to particlesthat are more mucoadhesive. For example, a luminal space such as thegastrointestinal tract is surrounded by a mucus-coated surface.Mucoadhesive particles delivered to such a space are typically removedfrom the luminal space and from the mucus-coated surface by thesubject's natural clearance mechanisms. The particles of the inventionwith reduced mucoadhesion may remain in the luminal space for relativelylonger periods compared to the mucoadhesive particles. This prolongedpresence may prevent or reduce clearance of the particles and/or mayallow for better distribution of the particles on the surface of thetissue. The prolonged presence may also affect the particle transportthrough the luminal space, e.g., the particles may distribute into themucus layer and may reach the underlying epithelium.

In certain embodiments, the core of the particles of the inventioncoated with the polymer of the coating may pass through mucus or amucosal barrier in a subject, exhibit prolonged retention, and/orincrease uniform distribution of the particles at mucosal surfaces,e.g., such substances are cleared more slowly (e.g., at least about 2times, about 5 times, about 10 times, or even at least about 20 timesmore slowly) from a subject's body as compared to a negative controlparticle of the invention.

The mobility of the particles of the invention in mucus may becharacterized in, e.g., the relative velocity and/or diffusivity of theparticles. In certain embodiments, the particles of the invention havecertain relative velocity, <V_(mean)>_(rel), which is defined asfollows:

$\begin{matrix}{{\langle V_{mean}\rangle}_{rel} = \frac{{\langle V_{mean}\rangle}_{Sample} - {\langle V_{mean}\rangle}_{{Negative}\mspace{14mu} {control}}}{{\langle V_{mean}\rangle}_{{Postitive}\mspace{14mu} {control}} - {\langle V_{mean}\rangle}_{{Negative}\mspace{14mu} {control}}}} & \left( {{Equation}\mspace{14mu} 1} \right)\end{matrix}$

wherein:

-   -   <V_(mean)> is the ensemble average trajectory-mean velocity;    -   V_(mean) is the velocity of an individual particle averaged over        its trajectory;    -   the sample is the particle of interest;    -   the negative control is a 200 nm carboxylated polystyrene        particle; and    -   the positive control is a 200 nm polystyrene particle densely        PEGylated with 2-5 kDa PEG.

The relative velocity can be measured by a multiple particle trackingtechnique. For instance, a fluorescent microscope equipped with a CCDcamera can be used to capture 15 s movies at a temporal resolution of66.7 ms (15 frames/s) under 100× magnification from several areas withineach sample for each type of particles: sample, negative control, andpositive control. The sample, negative control, and positive control maybe fluorescent particles to observe tracking. Alternativelynon-fluorescent particles may be coated with a fluorescent molecule, afluorescently tagged surface agent, or a fluorescently tagged polymer.An advanced image processing software (e.g., IMAGE PRO or METAMORPH) canbe used to measure individual trajectories of multiple particles over atime-scale of at least 3.335 s (50 frames).

In some embodiments, the particles of the invention have a relativevelocity of greater than or equal to about 0.3, greater than or equal toabout 0.5, greater than or equal to about 0.7, greater than or equal toabout 1.0, greater than or equal to about 1.5, or greater than or equalto about 2.0 in mucus. In some embodiments, particles of the inventionhave a relative velocity of less than about 10.0, less than about 6.0,less than about 2.0, less than about 1.5, less than about 1.0, or lessthan about 0.7 in mucus. Combinations of the above-noted ranges arepossible (e.g., a relative velocity of greater than or equal to about0.5 and less than about 6.0). Other ranges are also possible.

In certain embodiments, the particles of the invention diffuse throughmucus or a mucosal barrier at a greater rate or diffusivity thannegative control particles or corresponding particles (e.g., particlesthat are unmodified and/or not coated with a coating described herein).In some embodiments, the particles of the invention pass through mucusor a mucosal barrier at a rate of diffusivity that is at least about 10times, about 30 times, about 100 times, about 300 times, about 1000times, about 3000 times, about 10000 times higher than a controlparticle or a corresponding particle. In some embodiments, the particlesof the invention pass through mucus or a mucosal barrier at a rate ofdiffusivity that is less than about 10000 times higher, less than about3000 times higher, less than about 1000 times higher, less than about300 times higher, less than about 100 times higher, less than about 30times higher, or less than about 10 times higher than negative controlparticles or corresponding particles. Combinations of theabove-referenced ranges are also possible (e.g., at least about 10 timesand less than about 1000 times higher than negative control particles orcorresponding particles). Other ranges are also possible.

For the purposes of the comparisons described herein, the correspondingparticles may be approximately the same size, shape, and/or density asthe particles of the invention but lack the coating that makes theparticles of the invention mobile in mucus. In some embodiments, themeasurement of the geometric mean square displacement and rate ofdiffusivity of the particles (e.g., the corresponding particles andparticles of the invention) is based on a time scale of about 1 second,about 3 seconds, or about 10 seconds. Methods for determining thegeometric mean square displacement and rate of diffusivity are known inthe art. The particles of the invention may pass through mucus or amucosal barrier with a geometric mean squared displacement that is atleast about 10 times, about 30 times, about 100 times, about 300 times,about 1000 times, about 3000 times, about 10000 times higher thancorresponding particles or negative control particles. In someembodiments, the particles of the invention pass through mucus or amucosal barrier with a geometric mean squared displacement that is lessthan about 10000 times higher, less than about 3000 times higher, lessthan about 1000 times higher, less than about 300 times higher, lessthan about 100 times higher, less than about 30 times higher, or lessthan about 10 times higher than negative control particles orcorresponding particles. Combinations of the above-referenced ranges arealso possible (e.g., at least about 10 times and less than about 1000times higher than negative control particles or correspondingparticles). Other ranges are also possible.

In some embodiments, coated particles of the invention diffuse through amucosal barrier at a rate approaching the rate or diffusivity at whichthe particles can diffuse through water. In some embodiments, theparticles of the invention pass through a mucosal barrier at a rate ordiffusivity that is less than about 1/100, less than about 1/300, lessthan about 1/1000, less than about 1/3000, less than about 1/10,000 ofthe diffusivity that the particles diffuse through water under similarconditions. In some embodiments, particles of the invention pass througha mucosal barrier at a rate or diffusivity that is greater than or equalto about 1/10,000, greater than or equal to about 1/3000, greater thanor equal to about 1/1000, greater than or equal to about 1/300, orgreater than or equal to about 1/100 of the diffusivity that theparticles diffuse through water under similar conditions. Combinationsof the above-referenced ranges are also possible (e.g., greater than orequal to about 1/3000 and less than 1/300 the diffusivity that theparticles diffuse through water under similar conditions). Other rangesare also possible. The measurement of diffusivity may be based on a timescale of about 1 second, or about 0.5 second, or about 2 seconds, orabout 5 seconds, or about 10 seconds.

In some embodiments, the coated particles of the invention diffusethrough human cervicovaginal mucus at a diffusivity that is less thanabout 1/500 of the diffusivity that the particles diffuse through water.In some embodiments, the measurement of diffusivity is based on a timescale of about 1 second, or about 0.5 second, or about 2 seconds, orabout 5 seconds, or about 10 seconds.

In certain embodiments, the coated particles of the invention travelthrough mucus, such as human cervicovaginal mucus, at certain absolutediffusivities. For example, the particles of the invention may travel atdiffusivities of at least about 1×10⁻⁴ μm/s, about 3×10⁻⁴ μm/s, about1×10⁻³ μm/s, about 3×10⁻³ μm/s, about 1×10⁻² μm/s, about 3×10⁻² μm/s,about 1×10⁻¹ μm/s, about 3×10⁻¹ μm/s, about 1 μm/s, or about 3 μm/s. Insome embodiments, the particles may travel at diffusivities of less thanabout 3 μm/s, less than about 1 μm/s, less than about 3×10⁻¹ μm/s, lessthan about 1×10⁻¹ μm/s, less than about 3×10⁻² μm/s, less than about1×10⁻² μm/s, less than about 3×10⁻³ μm/s, less than about 1×10⁻³ μm/s,less than about 3×10⁻⁴ μm/s, or less than about 1×10⁻⁴ μm/s.Combinations of the above-referenced ranges are also possible (e.g.,greater than or equal to about 3×10⁻⁴ μm/s and less than about 1×10⁻¹μm/s). Other ranges are also possible. In some cases, the measurement ofdiffusivity is based on a time scale of about 1 second, or about 0.5second, or about 2 seconds, or about 5 seconds, or about 10 seconds.

It should be appreciated that while the mobility (e.g., relativevelocity and diffusivity) of the coated particles of the invention maybe measured in human cervicovaginal mucus, the mobility may be measuredin other types of mucus as well.

In certain embodiments, the particles of the invention comprisesurface-altering moieties at a given density. The surface-alteringmoieties may be the portions of a surface-altering agent that are, forexample, exposed to the solvent containing the particles. In oneexample, the hydrolyzed units/blocks of PVA may be surface-alteringmoieties of the surface-altering agent PVA. In another example, the PEGsegments may be surface-altering moieties of the surface-altering agentPEG-PPO-PEG. In some embodiments, the surface-altering moieties and/orsurface-altering agents are present at a density of at least about 0.001units or molecules per nm², at least about 0.003, at least about 0.01,at least about 0.03, at least about 0.1, at least about 0.3, at leastabout 1, at least about 3, at least about 10, at least about 30, atleast about 100 units or molecules per nm², or more units or moleculesper nm². In some cases, the surface-altering moieties and/orsurface-altering agents are present at a density of less than about 100units or molecules per nm², less than about 30, less than about 10, lessthan about 3, less than about 1, less than about 0.3, less than about0.1, less than about 0.03, or less than about 0.01 units or moleculesper nm². Combinations of the above-referenced ranges are possible (e.g.,a density of at least about 0.01 and less than about 1 units ormolecules per nm²). Other ranges are also possible. In some embodiments,the density values described herein are an average density as thesurface altering agent is in equilibrium with other components insolution.

Those skilled in the art would be aware of methods to estimate theaverage density of surface-altering moieties (see, for example, Budijonoet al., Colloids and Surfaces A: Physicochem. Eng. Aspects 2010, 360,105-110; Joshi et al., Anal. Chim. Acta 1979, 104, 153-160). Forexample, as described herein, the average density of surface-alteringmoieties can be determined using HPLC quantitation and DLS analysis. Asuspension of particles for which surface density determination is ofinterest is first sized using DLS: a small volume is diluted to anappropriate concentration (e.g., about 100 μg/mL), and the z-averagediameter is taken as a representative measurement of particle size. Theremaining suspension is then divided into two aliquots. Using HPLC, thefirst aliquot is assayed for the total concentration of core materialand for the total concentration of the surface-altering moiety. Againusing HPLC, the second aliquot is assayed for the concentration of freeor unbound surface-altering moiety. In order to get only the free orunbound surface-altering moiety from the second aliquot, the particles,and therefore any bound surface-altering moiety, are removed byultracentrifugation. By subtracting the concentration of the unboundsurface-altering moiety from the total concentration of surface-alteringmoiety, the concentration of bound surface-altering moiety can bedetermined. Since the total concentration of core material was alsodetermined from the first aliquot, the mass ratio between the corematerial and the surface-altering moiety can be determined. Using themolecular weight of the surface-altering moiety the number ofsurface-altering moiety to mass of core material can be calculated. Toturn this number into a surface density measurement, the surface areaper mass of core material needs to be calculated. The volume of theparticle is approximated as that of a sphere with the diameter obtainedfrom DLS allowing for the calculation of the surface area per mass ofcore material. In this way the number of surface-altering moieties persurface area can be determined.

In certain embodiments, the coated particles of the invention comprisesurface-altering moieties and/or agents that affect the zeta-potentialof the particle. The zeta potential of the particle may be, for example,at least about −100 mV, at least about −30 mV, at least about −10 mV, atleast about −3 mV, at least about 3 mV, at least about 10 mV, at leastabout 30 mV, or at least about 100 mV. The zeta potential of theparticle may also be, for example, less than about 100 mV, less thanabout 30 mV, less than about 10 mV, less than about 3 mV, less thanabout −3 mV, less than about −10 mV, less than about −30 mV, or lessthan about −100 mV. Combinations of the above-referenced ranges arepossible (e.g., a zeta-potential of at least about −30 mV and less thanabout 30 mV). Other ranges are also possible.

The coated particles of the invention may have any suitable shape and/orsize. In some embodiments, the particle has a shape substantiallysimilar to the shape of the core. In some embodiments, the particle is ananoparticle. In some embodiments, the particle is a microparticle. Aplurality of particles, in some embodiments, may also be characterizedby an average size (e.g., an average largest cross-sectional dimensionor average smallest cross-sectional dimension for a plurality ofparticles). A plurality of particles may have an average size of, forexample, less than about 10 μm, less than about 3 μm, less than about 1μm, less than about 500 nm, less than 400 nm, less than 300 nm, lessthan about 200 nm, less than about 100 nm, less than about 50 nm, lessthan about 30 nm, or less than about 10 nm. In some cases, a pluralityof particles may have an average size of, for example, at least about 10nm, at least about 30 nm, at least about 50 nm, at least about 100 nm,at least about 200 nm, at least about 300 nm, at least about 400 nm, atleast about 500 nm, at least about 1 μm, at least or at least about 3μm. Combinations of the above-referenced ranges are also possible (e.g.,an average size of at least about 30 nm and less than about 500 nm).Other ranges are also possible. In some embodiments, the sizes of thecores of the particles of the invention have a Gaussian-typedistribution. In some embodiments, the sizes of the particles of theinvention have a Gaussian-type distribution.

Pharmaceutical Agents

A particle or pharmaceutical composition of the invention may compriseat least one pharmaceutical agent of Formula (I) or Formula (VI). Incertain embodiments, the pharmaceutical agent described herein is apharmaceutically acceptable salt, solvate, hydrate, polymorph, tautomer,stereoisomer, isotopically labeled derivative, or prodrug of anotherpharmaceutical agent. In certain embodiments, the pharmaceutical agentis a co-crystal with another substance (e.g., a solvent, protein, oranother pharmaceutical agent). The pharmaceutical agent may be presentin the core and/or one or more coatings of the particle (e.g., dispersedthroughout the core and/or coating). In some embodiments, thepharmaceutical agent may be disposed on the surface of the particle(e.g., on the outer or inner surface of the one or more coatings or onthe surface of the core). The pharmaceutical agent may be containedwithin the particle and/or disposed in a portion of the particle usingcommonly known techniques (e.g., coating, adsorption, covalent linkage,and encapsulation). In some embodiments, the pharmaceutical agent ispresent during the formation of the core. In other embodiments, thepharmaceutical agent is not present during the formation of the core. Incertain embodiments, the pharmaceutical agent is present during thecoating of the core. In certain embodiments, the pharmaceutical agent isthe core of the particle.

In some embodiments, the pharmaceutical agent contained in a particle orpharmaceutical composition of the invention has a therapeutic and/orprophylactic effect in a mucosal tissue to be targeted. Non-limitingexamples of mucosal tissues include ophthalmic, respiratory (e.g.,including nasal, pharyngeal, tracheal, and bronchial membranes), oral(e.g., including the buccal and esophagal membranes and tonsil surface),gastrointestinal (e.g., including stomach, small intestine, largeintestine, colon, rectum), nasal, and genital (e.g., including vaginal,cervical and urethral membranes) tissues.

Any suitable number of pharmaceutical agents may be present in aparticle or pharmaceutical composition of the invention. For example, atleast 1, at least 2, at least 3, at least 4, at least 5, or morepharmaceutical agents may be present in the particle or pharmaceuticalcomposition of the invention. In certain embodiments, less than 10pharmaceutical agents are present in the particle or pharmaceuticalcomposition of the invention.

In certain embodiments, the pharmaceutical agent in the particles orpharmaceutical compositions of the invention is a compound of Formula(I) or a compound of Formula (VI) of the invention. The pharmaceuticalagent described herein (e.g., a compound of the invention) may beencapsulated in a polymer, a lipid, a protein, or a combination thereof.

Pharmaceutical Compositions

In another aspect, the present invention provides pharmaceuticalcompositions comprising the plurality of particles of a compound ofFormula (I) or a compound of Formula (VI) of the invention.

In certain embodiments, the pharmaceutical compositions are useful forthe delivery of a pharmaceutical agent described herein (e.g., acompound of the invention) through or to mucus or a mucosal surface in asubject. The pharmaceutical compositions may be delivered to the mucosalsurface in the subject and may pass through a mucosal barrier in thesubject (e.g., mucus), and/or may show prolonged retention and/orincreased uniform distribution of the particles of the invention at themucosal surface, e.g., due to reduced mucoadhesion. In certainembodiments, the pharmaceutical compositions are useful in increasingthe bioavailability of the pharmaceutical agent in the subject. Incertain embodiments, the pharmaceutical compositions are useful inincreasing the concentration of the pharmaceutical agent in the subject.In certain embodiments, the pharmaceutical compositions are useful inincreasing the exposure of the pharmaceutical agent in the subject.Moreover, the pharmaceutical compositions may be useful in treatingand/or preventing a disease (e.g., ocular disease) in a subject.

Moreover, the pharmaceutical compositions may be administeredparenterally as injections (intravenous, intramuscular, orsubcutaneous), drop infusion preparations, or suppositories. Forophthalmic applications, the pharmaceutical compositions may beadministered by injection (e.g., intraocular, intrastromal,intravitreal, or intracameral), or by the ophthalmic mucous membraneroute, the pharmaceutical compositions may be administered topically,such as suspensions (e.g., eye drops) or ointments.

The pharmaceutical composition of the invention may include one or morepharmaceutical agents described herein, such as a compound of theinvention. In certain embodiments, the pharmaceutical compositionincludes a plurality of particles of the invention that comprise one ormore pharmaceutical agents in the core and/or coating of the particles.In some embodiments, the ratio of the weight of each one of thepharmaceutical agents to the weight of each one of the one or moresurface-altering agents (e.g., PLURONIC® F127) present in thepharmaceutical composition is greater than or equal to about 1:100,greater than or equal to about 1:30, greater than or equal to about1:10, greater than or equal to about 1:3, greater than or equal to about1:1, greater than or equal to about 3:1, greater than or equal to about10:1, greater than or equal to about 30:1, or greater than or equal toabout 100:1. In some embodiments, the ratio of the weight of each one ofthe pharmaceutical agents to the weight of each one of the one or moresurface-altering agents in a pharmaceutical composition is less thanabout 100:1, less than about 30:1, less than about 10:1, less than about3:1, less than about 1:1, less than about 1:3: less than about 1:10,less than about 1:30, or less than about 1:100. Combinations of theabove-noted ranges are possible (e.g., a ratio of greater than or equalto about 1:1 and less than about 10:1). Other ranges are also possible.In certain embodiments, the ratio is about 1:1, about 2:1, or about10:1. In some embodiments, the pharmaceutical composition of theinvention includes the above-noted ranges for the ratio of the weight ofeach one of the pharmaceutical agents to the weight of each one of theone or more surface-altering agents during a formation process and/or adilution process described herein. In certain embodiments, thepharmaceutical composition includes the above-noted ranges for the ratioof the weight of each one of the pharmaceutical agents to the weight ofeach one of the one or more surface-altering agents immediately prior tothe pharmaceutical composition being administered to a subject orcontacted with a biological sample. The pharmaceutical agent may bepresent in the pharmaceutical composition of the invention in anysuitable amount, e.g., at least about 0.01 wt %, at least about 0.1 wt%, at least about 1 wt %, at least about 5 wt %, at least about 10 wt %,at least about 30 wt % of the pharmaceutical composition. In some cases,the pharmaceutical agent may be present in the pharmaceuticalcomposition at less than about 30 wt %, less than about 10 wt %, lessthan about 5 wt %, less than about 2 wt %, or less than about 1 wt % ofthe pharmaceutical composition. Combinations of the above-referencedranges are also possible (e.g., present in an amount of at least about0.1 wt % and less than about 10 wt % of the pharmaceutical composition).Other ranges are also possible. In certain embodiments, thepharmaceutical agent is about 0.1-2 wt % of the pharmaceuticalcomposition. In certain embodiments, the pharmaceutical agent is about2-20 wt % of the pharmaceutical composition. In certain embodiments, thepharmaceutical agent is about 0.2 wt %, about 0.4 wt %, about 1 wt %,about 2 wt %, about 5 wt %, or about 10 wt % of the pharmaceuticalcomposition.

In certain embodiments, the pharmaceutical composition includes aplurality of particles of the invention that comprise the chelatingagent in the core and/or coating of the particles.

In certain embodiments, the pharmaceutical composition includes aplurality of particles of the invention that comprise a tonicity agentin the core and/or coating of the particles.

It is appreciated in the art that the ionic strength of an inventivepharmaceutical composition that comprises a plurality of particles ofthe invention may affect the polydispersity of the plurality of theparticles. The ionic strength may also affect the colloidal stability ofthe plurality of the particles. For example, a relatively high ionicstrength of the pharmaceutical composition may cause the plurality ofparticles to coagulate and therefore may destabilize the pharmaceuticalcomposition. In some embodiments, the pharmaceutical composition isstabilized by repulsive inter-particle forces. For example, theplurality of particles may be electrically or electrostatically charged.Two charged particles may repel each other, preventing collision andaggregation. When the repulsive inter-particle forces weaken or becomeattractive, the plurality of particles may start to aggregate. Forinstance, when the ionic strength of the pharmaceutical composition isincreased to a certain level, the charges (e.g., negative charges) ofthe plurality of particles may be neutralized by the oppositely chargedions present in the pharmaceutical composition (e.g., Na⁺ ions insolution). As a result, the plurality of particles may collide and bondto each other to form aggregates (e.g., clusters or flocs) of largersizes. The formed aggregates of particles may also differ in size, andthus the polydispersity of the pharmaceutical composition may alsoincrease. For example, an inventive pharmaceutical compositioncomprising similarly-sized particles may become a pharmaceuticalcomposition comprising particles having various sizes (e.g., due toaggregation) when the ionic strength of the pharmaceutical compositionis increased beyond a certain level. In the course of aggregation, theaggregates may grow in size and eventually settle to the bottom of thecontainer, and the pharmaceutical composition is considered colloidallyunstable. Once the plurality of particles in a pharmaceuticalcomposition form aggregates, it is usually difficult to disrupt theaggregates into individual particles.

Certain pharmaceutical compositions of the invention show unexpectedproperties in that, among other things, the presence of one or moreionic tonicity agents (e.g., a salt, such as NaCl) in the pharmaceuticalcompositions at certain concentrations actually decreases or maintainsthe degree of aggregation of the particles present in the pharmaceuticalcompositions, and/or does not significantly increase aggregation. Incertain embodiments, the polydispersity of the pharmaceuticalcomposition decreases, is relatively constant, or does not change by anappreciable amount upon addition of one or more ionic tonicity agentsinto the pharmaceutical composition. For example, in some embodiments,the polydispersity of a pharmaceutical composition is relativelyconstant in the presence of added ionic strength and/or when the addedionic strength of the pharmaceutical composition is kept relativelyconstant or increased (e.g., during a formation and/or dilution processdescribed herein). In certain embodiments, when the ionic strengthincreases by at least 50%, the polydispersity increases by less thanabout 300%, less than about 100%, less than about 30%, less than about10%, less than about 3%, or less than about 1%. In certain embodiments,when the ionic strength is increased by at least 50%, the polydispersityincreases by greater than or equal to about 1%, greater than or equal toabout 3%, greater than or equal to about 10%, greater than or equal toabout 30%, or greater than or equal to about 100%. Combinations of theabove-noted ranges are possible (e.g., an increase in polydispersity ofless than 30% and greater than or equal to 3%). Other ranges are alsopossible.

The ionic strength of a pharmaceutical composition of the invention maybe controlled (e.g., increased, decreased, or maintained) through avariety of means, such as the addition of one or more ionic tonicityagents (e.g., a salt, such as NaCl) to the pharmaceutical composition.In certain embodiments, the ionic strength of a pharmaceuticalcomposition of the invention is greater than or equal to about 0.0003 M,greater than or equal to about 0.001 M, greater than or equal to about0.003 M, greater than or equal to about 0.01 M, greater than or equal toabout 0.03 M, greater than or equal to about 0.1 M, greater than orequal to about 0.3 M, greater than or equal to about 1 M, greater thanor equal to about 3 M, or greater than or equal to about 10 M. Incertain embodiments, the ionic strength of a pharmaceutical compositionof the invention is less than about 10 M, less than about 3 M, less thanabout 1 M, less than about 0.3 M, less than about 0.1 M, less than about0.03 M, less than about 0.01 M, less than about 0.003 M, less than about0.001 M, or less than about 0.0003 M. Combinations of the above-notedranges are possible (e.g., an ionic strength of greater than or equal toabout 0.01 M and less than about 1 M). Other ranges are also possible.In certain embodiments, the ionic strength of a pharmaceuticalcomposition of the invention is about 0.1 M, about 0.15 M, or about 0.3M.

In certain embodiments, the polydispersity of a pharmaceuticalcomposition does not change upon addition of one or more ionic tonicityagents into the pharmaceutical composition. In certain embodiments, thepolydispersity does not significantly increase upon addition of one ormore ionic tonicity agents into the pharmaceutical composition. Incertain embodiments, the polydispersity increases to a level describedherein upon addition of one or more ionic tonicity agents into thepharmaceutical composition.

The polydispersity of an inventive pharmaceutical composition thatcomprises a plurality of particles of the invention may be measured bythe polydispersity index (PDI). In certain embodiments, the PDI of thepharmaceutical composition is less than about 1, less than about 0.8,less than about 0.6, less than about 0.4, less than about 0.3, less thanabout 0.2, less than about 0.15, less than about 0.1, less than about0.05, less than about 0.01, or less than about 0.005. In certainembodiments, the PDI of the pharmaceutical composition is greater thanor equal to about 0.005, greater than or equal to about 0.01, greaterthan or equal to about 0.05, greater than or equal to about 0.1, greaterthan or equal to about 0.15, greater than or equal to about 0.2, greaterthan or equal to about 0.3, greater than or equal to about 0.4, greaterthan or equal to about 0.6, greater than or equal to about 0.8, orgreater than or equal to about 1. Combinations of the above-noted rangesare possible (e.g., a PDI of greater than or equal to about 0.1 and lessthan about 0.5). Other ranges are also possible. In certain embodiments,the PDI of the pharmaceutical composition is about 0.1, about 0.15, orabout 0.2. In certain embodiments, the pharmaceutical composition ishighly dispersible and does not tend to form aggregates. Even when theparticles do form aggregates, the aggregates may be easily broken upinto individual particles without rigorously agitating thepharmaceutical composition.

Methods of Preparing Particles and Pharmaceutical Compositions Thereof

In one aspect, the present invention provides methods of preparing theparticles of the invention. Methods of preparing similar particles havebeen described in U.S. patent application Ser. No. 13/886,493, filed May3, 2013, and U.S. Ser. No. 13/886,602, filed May 3, 2013, and U.S. Ser.No. 13/886,658, filed May 3, 2013, each of which is incorporated byreference herein in its entirety.

The core of the particle may be formed by any suitable method. Suitablemethods may include, for example, top-down techniques, i.e. techniquesbased on size reduction of relatively large particles into smallerparticles (e.g., milling or homogenization) or bottom-up techniques,i.e. techniques based on the growth of particles from smaller particlesor individual molecules (e.g., precipitation or spray-freezing intoliquid).

In some embodiments, the core of the particle may be coated with acoating. For example, the core may be provided or formed in a firststep, and then the core may be coated in a second step. In someembodiments, the core particle is formed and coated substantiallysimultaneously (e.g., in a single step).

In some embodiments, the particle is formed by a method that involvesusing a formulation process, a milling process, and/or a dilutionprocess. In certain embodiments, a method of forming the particleincludes a milling process, optionally with a formulation process and/ora dilution process. A formulation process may be used to form asuspension comprising a core material, one or more surface-alteringagents, and other components, such as solvents, tonicity agents,chelating agents, salts, and/or buffers (e.g., a sodium citrate andcitric acid buffer), each of which is as described herein. Theformulation process may be performed using a formulation vessel. Thecore material and other components may be added into the formulationvessel at the same time or different times. A mixture of the corematerial and/or one or more other components may be stirred and/orshaken, or otherwise agitated in the vessel to facilitate suspending thecomponents to form the suspension. The temperature and/or pressure ofthe core material, other components, and/or mixture may also beindividually increased or decreased to facilitate the suspendingprocess. In some embodiments, the core material and other components areprocessed as described herein in the formulation vessel under an inertatmosphere (e.g., nitrogen or argon) and/or protected from light. Thesuspension obtained from the formulation vessel may be subsequentlysubject to a milling process which may be followed by a dilutionprocess.

In some embodiments involving a core comprising a solid material (e.g.,crystalline compound of the invention) a milling process may be used toreduce the size of the solid material to form particles in a micrometerto nanometer size range. The milling process may be performed using amill or other suitable apparatus. Dry and wet milling processes such asjet milling, cryo-milling, ball milling, media milling, sonication, andhomogenization are known and can be used in methods of the invention.For example, in a wet milling process, a suspension of the solidmaterial to be used to form the core (“core material”) is agitated withor without excipients to reduce the size of the core to be formed. Drymilling is a process wherein the core material is mixed with millingmedia with or without excipients to reduce the size of the core to beformed. In a cyro-milling process, a suspension of the core material ismixed with milling media with or without excipients under cooledtemperatures. In certain embodiments, when surface-altering agents areemployed, a suspension comprising coated particles is obtained from themilling process. In certain embodiments, when surface-altering agentsare not employed, a suspension comprising uncoated particles is obtainedfrom the milling process.

The suspension of particles (coated or uncoated) of the inventionobtained from a milling process may be further processed with a dilutionprocess. A dilution process may be used to achieve a target dosingconcentration by diluting a suspension of particles that were formedduring a milling process, with or without surface-altering agents and/orother components. In certain embodiments, when a suspension of coatedparticles that comprise a first surface-altering agent is processed witha dilution process involving a second surface-altering agent, asuspension of coated particles that comprise the second surface-alteringagent is obtained from the dilution process. In certain embodiments,when a suspension of coated particles that comprise a surface-alteringagent is processed with a dilution process involving no or the samesurface-altering agent, a suspension of coated particles that comprisethe surface-altering agent is obtained from the dilution process. Incertain embodiments, when a suspension of uncoated particles isprocessed with a dilution process involving a surface-altering agent, asuspension of coated particles comprising the surface-altering agent isobtained from the dilution process. The dilution process may beperformed using a product vessel or any other suitable apparatus. Incertain embodiments, the suspension of the particles is diluted, i.e.,mixed or otherwise processed with a diluent, in the product vessel. Thediluent may contain solvents, surface-altering agents, tonicity agents,chelating agents, salts, or a combination thereof, as described herein.The suspension and the diluent may be added into the product vessel atthe same time or different times. In certain embodiments when thesuspension is obtained from a milling process involving milling media,the milling media may be separated from the suspension before thesuspension is added into the product vessel. The suspension, thediluent, or the mixture of the suspension and the diluent may be stirredand/or shaken, or otherwise agitated, to form the particles and/orpharmaceutical compositions of the invention. The temperature and/orpressure of the suspension, the diluent, or the mixture may also beindividually increased or decreased to form the coated particles. Insome embodiments, the suspension and the diluent are processed in theproduct vessel under an inert atmosphere (e.g., nitrogen or argon)and/or protected from light.

In some embodiments, the core and/or coated particles may be produced bymilling of a solid material (e.g., a pharmaceutical agent) in thepresence of one or more surface-altering agents. Small particles of asolid material may require the presence of one or more surface-alteringagents, which may function as a stabilizer in some embodiments, in orderto stabilize a suspension of particles without agglomeration oraggregation in a liquid solution. In some such embodiments, thestabilizer may act as a surface-altering agent, forming the coatedparticles of the invention.

As described herein, a method of forming the core and/or the coatedparticles, may involve choosing a surface-altering agent that issuitable for both milling and forming a coating on the core, wherein thecoating renders the particle mucus penetrating.

In a wet milling process, milling may be performed in a dispersion(e.g., an aqueous dispersion) containing at least one surface-alteringagent, a grinding medium, a solid to be milled (e.g., a solidpharmaceutical agent), and a solvent. The solvent described hereinincludes a single solvent or a mixture of different solvents. Anysuitable amount of a surface-altering agent can be included in thesolvent. In some embodiments, the surface-altering agent may be presentin the solvent in an amount of at least about 0.001% (wt % or % weightto volume (w:v)), at least about 0.01%, at least about 0.1%, at leastabout 1%, at least about 3%, at least about 10%, at least about 30%, orat least about 60% of the solvent. In some cases, the surface-alteringagent may be present in the solvent in an amount of about 100% (e.g., inan instance where the surface-altering agent is the solvent). In otherembodiments, the surface-altering agent may be present in the solvent inan amount of less than about 100%, less than about 60%, 1 less thanabout 30%, less than about 10%, less than about 3%, or less than about1% of the solvent. Combinations of the above-referenced ranges are alsopossible (e.g., an amount of less than about 3% and at least about 1% ofthe solvent). Other ranges are also possible. In certain embodiments,the surface-altering agent is present in the solvent in an amount ofabout 0.01-2%, about 0.2-20%, about 0.1%, about 0.4%, about 1%, about2%, about 5%, or about 10% of the solvent.

The particular range chosen may influence factors that may affect theability of the particles to penetrate mucus such as the stability of thecoating of the surface-altering agent on the particle surface, theaverage thickness of the coating of the surface-altering agent on theparticles, the orientation of the surface-altering agent on theparticles, the density of the surface altering agent on the particles,the ratio of the surface-altering agent to pharmaceutical agent, theconcentration of the pharmaceutical agent, the size, dispersibility, andpolydispersity of the particles formed, and the morphology of theparticles formed.

The pharmaceutical agent may be present in the solvent in any suitableamount. In some embodiments, the pharmaceutical agent is present in anamount of at least about 0.001% (wt % or % weight to volume (w:v)), atleast about 0.01%, at least about 0.1%, at least about 1%, at leastabout 3%, at least about 10%, at least about 30%, or at least about 60%of the solvent. In some cases, the pharmaceutical agent may be presentin the solvent in an amount of less than about 100%, less than about60%, less than about 30%, less than about 10%, less than about 3%, orless than about 1% of the solvent. Combinations of the above-referencedranges are also possible (e.g., an amount of less than about 30% and atleast about 1% of the solvent).

The ratio of surface-altering agent to pharmaceutical agent in a solventmay also vary. In some embodiments, the ratio of the surface-alteringagent to pharmaceutical agent is at least about 0.001:1 (weight ratio,molar ratio, or w:v), at least about 0.01:1, at least about 0.01:1, atleast about 1:1, at least about 2:1, at least about 3:1, at least about5:1, at least about 10:1, at least about 30:1, at least about 100:1, orat least about 1000:1. In some embodiments, the ratio of thesurface-altering agent to pharmaceutical agent is less than 1000:1(weight ratio, molar ratio, or w:v), less than about 100:1, less thanabout 30:1, less than about 10:1, less than about 5:1, less than about3:1, less than about 2:1, less than about 1:1, or less than about 0.1:1.Combinations of the above-referenced ranges are possible (e.g., a ratioof at least about 5:1 and less than about 30:1). Other ranges are alsopossible.

The surface-altering agents described herein that may act as stabilizersmay be, for example, polymers or surfactants. Examples of polymersinclude those suitable for use in the coating of the particles of theinvention, such as poly(vinyl alcohol) and PLURONICS®. Examples ofsurfactants include L-α-phosphatidylcholine (PC),1,2-dipalmitoylphosphatidycholine (DPPC), oleic acid, sorbitantrioleate, sorbitan mono-oleate, sorbitan monolaurate, polyoxyethylenesorbitan monolaurate, polyoxyethylene sorbitan monooleate, naturallecithin, oleyl polyoxyethylene ether, stearyl polyoxyethylene ether,lauryl polyoxyethylene ether, block copolymers of oxyethylene andoxypropylene, synthetic lecithin, diethylene glycol dioleate,tetrahydrofurfuryl oleate, ethyl oleate, isopropyl myristate, glycerylmonooleate, glyceryl monostearate, glyceryl monoricinoleate, cetylalcohol, stearyl alcohol, polyethylene glycol, cetyl pyridiniumchloride, benzalkonium chloride, olive oil, glyceryl monolaurate, cornoil, cotton seed oil, and sunflower seed oil.

A stabilizer used for milling may form the coating of a particle of theinvention, wherein the coating renders the particle mucus penetrating.The stabilizer may also be exchanged with one or more othersurface-altering agents after the particle has been formed. For example,a first stabilizer/surface-altering agent may be used during a millingprocess and may form a first coating of the particle of the invention,and all or part of the first stabilizer/surface-altering agent may thenbe exchanged with a second stabilizer/surface-altering agent to form asecond coating of the particle. In some embodiments, the secondstabilizer/surface-altering agent may render the particle mucuspenetrating more than the first stabilizer/surface-altering agent. Insome embodiments, a particle comprising multiple coatings that includemultiple surface-altering agents is formed by a method of the invention.

Any suitable grinding medium can be used for milling. In someembodiments, a ceramic and/or polymeric material and/or a metal can beused. Examples of suitable materials include zirconium oxide, siliconcarbide, silicon oxide, silicon nitride, zirconium silicate, yttriumoxide, glass, alumina, alpha-alumina, aluminum oxide, polystyrene,poly(methyl methacrylate), titanium, and steel. A grinding medium mayhave any suitable size. For example, the grinding medium may have anaverage diameter of at least about 0.1 mm, at least about 0.2 mm, atleast about 0.5 mm, at least about 0.8 mm, at least about 1 mm, at leastabout 2 mm, or at least about 5 mm. In some cases, the grinding mediummay have an average diameter of less than about 5 mm, less than about 2mm, less than about 1 mm, less than about 0.8, less than about 0.5 mm,or less than about 0.2 mm. Combinations of the above-referenced rangesare also possible (e.g., an average diameter of at least about 0.5millimeters and less than about 1 mm). Other ranges are also possible.

A solvent may be used for milling. The choice of the solvent suitablefor milling may depend on factors like the solid material (e.g., a solidpharmaceutical agent) being milled, the particular type ofstabilizer/surface-altering agent (e.g., one that may render theparticle mucus penetrating), and the grinding material. The solventsuitable for milling may be one of those solvents that do notsubstantially dissolve the solid material or the grinding material, butdissolve the stabilizer/surface-altering agent to a suitable degree.Examples of the solvents suitable for milling include water, aqueoussolutions, buffered solutions, alcohols (e.g., ethanol, methanol, andbutanol), and mixtures thereof, each of which may optionally includeother components, such as one or more pharmaceutical excipients,polymers, pharmaceutical agents, salts, preservative agents, viscositymodifiers, tonicity modifiers, taste masking agents, antioxidants, andpH modifiers. In some embodiments, the solvent suitable for milling isan organic solvent.

A pharmaceutical agent described herein (e.g., a compound of theinvention) may have a suitable solubility in a solvent suitable formilling, such as a solubility in one or more ranges described herein foraqueous solubility or for solubility in a coating solution. Apharmaceutical agent having a relatively low solubility in a solvent(e.g., water or a coating solution) may be preferred because a millingprocess described herein typically requires a material (e.g., apharmaceutical agent) to be in a solid form in order for the material tobe milled. In some cases, if the material to be milled has a relativelyhigh soluble in a solvent (e.g., water or a coating solution) used inthe milling process, milling may not be conducted because significant orcomplete dissolution of the material to be milled in the solvent willoccur. In certain embodiments, a relatively high solubility of a solidmaterial (e.g., a solid pharmaceutical agent) in a solvent is at leastabout 1 mg/mL, at least about 3 mg/mL, or at least about 10 mg/mL at 25°C. In certain embodiments, a relatively low solubility of a substance(e.g., a pharmaceutical agent) in a solvent is less than about 1 mg/mL,less than about 0.3 mg/mL, less than about 0.1 mg/mL, less than about0.03 mg/mL, less than about 0.01 mg/mL, less than about 0.003 mg/mL, orless than about 0.001 mg/mL at 25° C. The solid material may have theseor other ranges of solubilities at any point throughout the pH range(e.g., from pH 1 to pH 14). A pharmaceutical agent that has a relativelyhigh solubility in the solvent used in the milling process may bemodified to form a prodrug of the pharmaceutical agent. The prodrug mayhave a relatively low solubility and thus may be suitable for themilling process. Upon or after the particles or pharmaceuticalcompositions comprising the prodrug are administered to a subject, theprodrug may be converted and form or, in other words, “release,” thepharmaceutical agent.

In other embodiments, the core and/or coated particles may be formed byan emulsification process or technique (emulsification) known in theart. See, e.g., U.S. patent application Ser. No. 13/886,602. The coreand/or coated particles may also be formed by a precipitation process ortechnique (precipitation). Precipitation techniques (e.g.,microprecipitation, nanoprecipitation, crystallization, and controlledcrystallization) may involve forming a first solution comprising thematerial that is to form the core (e.g., a pharmaceutical agent) and afirst solvent, wherein the material has a relatively high solubility inthe first solvent. The first solution may be added to a second solutioncomprising a second solvent that is an anti-solvent, in which thematerial has a relatively low solubility, thereby forming a plurality ofparticles comprising the material. In certain embodiments, the secondsolvent is miscible with the first solvent. In some embodiments, one ormore surface-altering agents and/or surfactants may be present in thefirst and/or second solutions. A coating may be formed during theprocess of precipitating the core (e.g., the coating of the particlesmay be formed substantially simultaneously when the precipitation isperformed) to form the coated particles of the invention.

In other embodiments, the core of the particles of the invention isfirst formed using a precipitation technique, following by coating ofthe core with a surface-altering agent to form the coated particles ofthe invention.

In some embodiments, a precipitation technique may be used to formpolymeric core of the particles of the invention with or without apharmaceutical agent. Generally, a precipitation technique involvesdissolving a polymer that is to form the core in a first solvent, in thepresence or absence of a pharmaceutical agent, to form a solution. Thesolution is then added to a second solvent that is an anti-solvent andis miscible with the first solvent, in the presence or absence of one ormore excipients, to form the core of the particles. In some embodiments,precipitation is useful for preparing a polymeric core comprising one ormore pharmaceutical agents having a relatively low aqueous solubility.

The precipitation described herein involves the use of a first solvent.Examples of suitable first solvents for precipitation include organicsolvents (e.g., acetone, acetonitrile, dimethylformamide,dimethysulfoxide, N-methyl-2-pyrrolidone, 2-pyrrolidone, andtetrahydrofuran) and inorganic solvents.

The precipitation described herein also involves the use of a secondsolvent. In certain embodiments, the second solvent suitable forprecipitation is an anti-solvent. Examples of second solvents suitablefor precipitation include the solvents described herein that may be usedfor milling. In some embodiments, the second solvents suitable forprecipitation is water, an aqueous solution (e.g., a buffered solution),an alcohol (e.g., methanol, ethanol, propanol, or butanol), or a mixturethereof, optionally including one or more other components, such aspharmaceutical excipients, polymers, and pharmaceutical agents.

Surface-altering agents for the emulsification and precipitationdescribed herein may be polymers or surfactants, including thesurface-altering agents described herein that may be used for milling.

Examples of polymers suitable for forming all or part of the core of theparticles of the invention by the emulsification or precipitationinclude the polymers (including copolymers) described herein.

In some embodiments, a precipitation technique may be used to formparticles comprised predominantly of a pharmaceutical agent (e.g., acompound of the invention). In certain embodiments, the particles of theinvention formed by the precipitation technique comprise predominantlyof a pharmaceutical agent that is a nanocrystal. Generally, such aprecipitation technique involves dissolving the pharmaceutical agentthat is to form the core in a first solvent, which is then added to asecond solvent that is an anti-solvent, in which the pharmaceuticalagent has a relatively low solubility, in the presence or absence of oneor more pharmaceutical excipients, to form the core or uncoatedparticle. In some embodiments, this technique may be useful forpreparing, for example, particles of pharmaceutical agents that areslightly soluble (1-10 mg/mL), very slightly soluble (0.1-1 mg/mL) orpractically insoluble (<0.1 mg/mL) in aqueous solutions (e.g., agentshaving a relatively low aqueous solubility).

A pharmaceutical agent described herein (e.g., a compound of theinvention) may have a suitable solubility in the first and secondsolvents suitable for precipitation, such as a solubility in one or moreranges described herein for aqueous solubility or for solubility in acoating solution. A pharmaceutical agent having a relatively highsolubility in the first solvent (e.g., an organic solvent) may bepreferred. In certain embodiments, the pharmaceutical agentsubstantially or completely dissolves in the first solvent. Apharmaceutical agent having a relatively low solubility in the secondsolvent (e.g., water or a coating solution) may also be preferred. Incertain embodiments, the solubility of the pharmaceutical agent in amixture of the first and second solvents is lower than the solubility ofthe pharmaceutical agent in the first solvent. The relatively highsolubility and relatively low solubility are as described herein. Apharmaceutical agent that has a relatively high solubility in the secondsolvent may be modified to form a prodrug of the pharmaceutical agent.The prodrug may have a relatively low solubility in the second solventand still have a relatively high solubility in the first solvent andthus may be suitable for precipitation. Upon or after the particles orpharmaceutical compositions comprising the prodrug are administered to asubject, the prodrug may be converted and form or, in other words,“release,” the pharmaceutical agent.

Precipitation by formation of a salt or complex may also be used to formparticles comprised predominantly of a salt or complex of apharmaceutical agent. In certain embodiments, the particles formed bythis specific precipitation technique comprise predominantly of apharmaceutical agent that is a nanocrystal. Generally, precipitation byformation of a salt or complex involves dissolving a pharmaceuticalagent that is to form the core in a solvent, in the presence or absenceof one or more excipients, followed by the addition of a counterion or acomplexing agent, which forms a salt or a complex with thepharmaceutical agent to form the core. All counterions described hereinare contemplated to be within the scope of the invention. This techniquemay be useful for preparing particles comprising pharmaceutical agentsthat have a relatively high solubility in the second solvent (e.g.,water or a coating solution). In certain embodiments, the pharmaceuticalagent has a relatively high solubility in the second solvent, and thesalt or complex of the pharmaceutical agent has a relatively lowsolubility in the second solvent. The relatively high solubility andrelatively low solubility are as described herein. In some embodiments,pharmaceutical agents having one or more charged or ionizable groupsinteract with a counterion (e.g., a cation or an anion) to form a saltor complex.

A variety of different acids may be used in a precipitation processinvolving formation of a salt or complex. Examples of acids suitable forprecipitation include deconoic acid, hexanoic acid, mucic acid, octanoicacid. In other embodiments, a suitable acid may include acetic acid,adipic acid, L-ascorbic acid, L-aspartic acid, capric acid (decanoicacid), carbonic acid, citric acid, fumaric acid, galactaric acid,D-glucoheptonic acid, D-gluconic acid, D-glucuronic acid, glutamic acid,glutaric acid, glycerophosphoric acid, glycolic acid, hippuric acid,hydrochloric acid, DL-lactic acid, lauric acid, maleic acid, (−)-L-malicacid, palmitic acid, phosphoric acid, sebacic acid, stearic acid,succinic acid, sulfuric acid, (+)-L-tartaric acid, or thiocyanic acid.In other embodiments, a suitable acid may include alginic acid,benzenesulfonic acid, benzoic acid, (+)-camphoric acid, caprylic acid(octanoic acid), cyclamic acid, dodecylsulfuric acid,ethane-1,2-disulfonic acid, ethanesulfonic acid, ethanesulfonic acid,2-hydroxy-, gentisic acid, glutaric acid, 2-oxo-, isobutyric acid,lactobionic acid, malonic acid, methanesulfonic acid,naphthalene-1,5-disulfonic acid, naphthalene-2-sulfonic acid,2-naphthoic acid, 1-hydroxy-, nicotinic acid, oleic acid, orotic acid,oxalic acid, pamoic acid, (embonic acid), propionic acid,(−)-L-pyroglutamic acid, or p-toluenesulfonic acid. In yet otherembodiments, a suitable acid may include acetic acid, 2,2-dichloro-,benzoic acid, 4-acetamido-, (+)-camphor-10-sulfonic acid, caproic acid(hexanoic acid), cinnamic acid, formic acid, hydrobromic acid,DL-mandelic acid, nitric acid, salicylic acid, salicylic acid, 4-amino-,and undecylenic acid (undec-10-enoic acid). Mixtures of two or moreacids can also be used.

A variety of different bases may also be used in a precipitation processinvolving formation of a salt or complex. Examples of bases suitable forprecipitation include ammonia, L-arginine, calcium hydroxide, choline,glucamine, N-methyl-, lysine, magnesium hydroxide, potassium hydroxide,or sodium hydroxide. In other embodiments, a suitable base may includebenethamine, benzathine, betaine, deanol, diethylamine, ethanol,2-(diethylamino)-, hydrabamine, morpholine, 4-(2-hydroxyethyl)-,pyrrolidine, 1-(2-hyroxyethyl)-, or tromethamine. In other embodiments,a suitable base may include diethanolamine (2,2′-iminobis(ethanol)),ethanolamine (2-aminoethanol), ethylenediamine, 1H-imidazole,piperazine, triethanolamine (2,2′,2″-nitrilotris(ethanol)), and zinchydroxide. Mixtures of two or more bases can also be used.

Examples of solvents suitable for precipitation involving formation of asalt or complex include the solvents described herein that may be usedfor milling. In some embodiments, the first or second solvent suitablefor precipitation involving formation of a salt or complex is water, anaqueous solution (e.g., a buffered solution), an alcohol (e.g.,methanol, ethanol, propanol, or butanol), or a mixture thereof,optionally including one or more other components, such aspharmaceutical excipients, polymers, and pharmaceutical agents.

The first or second solvent suitable for precipitation may include oneor more surface-altering agents as described herein, and therefore, acoating comprising the one or more surface-altering agents may be formedaround the core to provide the coated particles of the invention as theyprecipitate out of solution. The one or more surface-altering agents maybe present in the first or second solvent at any suitable concentration,such as a concentration of at least about 0.001% (w/v), at least about0.003% (w/v), at least about 0.01% (w/v), at least about 0.03% (w/v), atleast about 0.1% (w/v), at least about 0.3% (w/v), at least about 1%(w/v), or at least about 3% (w/v). In some embodiments, the one or moresurface-altering agents are present in the first or second solvent at aconcentration of less than about 3% (w/v), less than about 1% (w/v),less than about 0.3% (w/v), less than about 0.1% (w/v), less than about0.05% (w/v), less than about 0.01% (w/v), or less than about 0.003%(w/v). Combinations of the above-referenced ranges are also possible(e.g., a concentration of at least about 0.01 (w/v) and less than about1% (w/v). Other ranges are also possible. In certain embodiments, theone or more surface-altering agents are present in the first solvent butabsent in the second solvent. In certain embodiments, the one or moresurface-altering agents are present in the second solvent but absent inthe first solvent. In certain embodiments, the one or moresurface-altering agents are present in both the first and secondsolvents.

Another exemplary method of forming the core and/or coated particle is afreeze-drying process or technique known in the art. See, e.g., U.S.patent application Ser. No. 13/886,602.

Other methods of forming core particles are also possible. For example,additional techniques of forming the core and/or coated particlesinclude coacervation-phase separation, melt dispersion, interfacialdeposition, in situ polymerization, self-assembly of macromolecules(e.g., formation of polyelectrolyte complexes orpolyelectrolyte-surfactant complexes), spray-drying andspray-congealing, electro-spray, air suspension coating, pan and spraycoating, freeze-drying, air drying, vacuum drying, fluidized-bed drying,precipitation (e.g., nanoprecipitation, microprecipitation), criticalfluid extraction, and lithographic approaches (e.g., soft lithography,step and flash imprint lithography, interference lithography, andphotolithography). Combinations of the methods described herein are alsopossible. In some embodiments, a core of a pharmaceutical agent is firstformed by precipitation, and then the size of the core is reduced by amilling process, optionally a coating is form on the core by the millingprocess.

Following the formation of the core of the particles including apharmaceutical agent, the core may be optionally exposed to a solutioncomprising a (second) surface-altering agent that may associate withand/or coat the core. In embodiments in which the pharmaceutical agentalready includes a coating of a first surface-altering agent, all orpart of the first surface-altering agent may be exchanged with a secondsurface-altering agent. In some embodiments, the second surface-alteringagent renders the particle mucus penetrating more than the firstsurface-altering agent does. In some embodiments, a particle having acoating including multiple surface-altering agents is formed (e.g., in asingle layer or in multiple layers). In some embodiments, a particlehaving multiple coatings (e.g., each coating optionally comprisingdifferent surface-altering agents) may be formed. In some embodiments,the coating is in the form of a monolayer of a surface-altering agent.Other configurations are also possible.

In any of the methods described herein, a coating comprising asurface-altering agent may be formed on a core of the particles of theinvention by incubating the core in a solution including thesurface-altering agent for a period of at least about 1 minute, at leastabout 3 minutes, at least about 10 minutes, at least about 20 minutes,at least about 30 minutes, at least about 60 minutes, or more. In somecases, incubation may take place for a period of less than about 10hours, less than about 3 hours, or less than about 60 minutes.Combinations of the above referenced ranges are also possible (e.g., anincubation period of less than 60 minutes and at least about 1 minute).

Methods of Treating/Uses

The present invention provides compounds, particles, and compositionsthereof for treating a disease. In some embodiments, methods of treatinga disease in a subject are provided which comprise administering aneffective amount of a compound of Formula (I) of a compound of Formula(VI) to a subject in need of treatment. In certain embodiments, theeffective amount is a therapeutically effective amount. In certainembodiments, the effective amount is a prophylactically effectiveamount. In certain embodiments, the subject is suffering from a growthfactor-associated disease. In certain embodiments, the subject issusceptible to a growth factor-associated disease. In certainembodiments, the subject is at risk of developing macular degeneration.

The present invention further provides methods of inhibiting VEGFactivity or signaling in a cell. In some embodiments, such methodscomprise contacting a cell with an effective amount of a compound ofFormula (I) or a compound of Formula (VI). In some embodiments, the cellis in vitro. In some embodiments, the cell is in vivo.

As used herein, the term “growth factor-associated disease” means anydisease where growth factors are known to play a role. Accordingly, insome embodiments, the present disclosure relates to treating diseases inwhich growth factors are known to play a role. Such diseases includeproliferative diseases, eye diseases, dermatological diseases,inflammation diseases, and metabolic diseases.

In some embodiments, the present disclosure provides methods of treatinga disease comprising contacting a biological sample with an effectiveamount of a compound of Formula (I). In other embodiments, the presentdisclosure provides methods of treating a disease comprising contactinga biological sample with an effective amount of a compound of Formula(VI). In certain embodiments, the biological sample includes a cell ortissue. In some embodiments, the methods comprise inhibiting growthfactor signaling in a cell, tissue, or subject. In some embodiments, thebiological sample is an ocular tissue. In certain embodiments, themethod is an in vitro method. In certain embodiments, the method is anin vivo method. It will be understood by one of ordinary skill in theart that levels of inhibition are not necessary to be 100%. The levelsof inhibition can be at least 10% inhibition, about 10% to about 25%inhibition, about 25% to about 50% inhibition, about 50% to about 75%inhibition, at least 50% inhibition, at least 75% inhibition, about 80%inhibition, about 90% inhibition, or greater than 90% inhibition.

In some embodiments, the present disclosure provides methods to treat orprevent an ocular disease, i.e., a disease, ailment, or condition thataffects or involves the eye or one or more of the parts or regions ofthe eye.

In some embodiments, the present disclosure provides a method to treator prevent an ocular disease at the front of the eye of a subject. Afront of the eye ocular disease includes post-surgical inflammation,uveitis, infections, aphakia, pseudophakia, astigmatism, blepharospasm,cataract, conjunctival diseases, conjunctivitis, corneal diseases,corneal ulcer, dry eye, dry eye syndromes, eyelid diseases, lacrimalapparatus diseases, lacrimal duct obstruction, myopia, presbyopia, pupildisorders, corneal neovascularization, refractive disorders andstrabismus. Glaucoma can be considered to be a front of the eye ocularcondition in some embodiments because a clinical goal of glaucomatreatment can be to reduce a hypertension of aqueous fluid in theanterior chamber of the eye (i.e., reduce intraocular pressure).

In some embodiments, the present disclosure provides a method to targetand/or treat portions within the posterior portion or back of the eye,such as the retina, the choroid, and/or the sclera, of a subject. Ingeneral, a back of the eye or posterior ocular disease is a disease,ailment, or condition which primarily affects or involves a tissue orfluid at the back of the eye, as described herein. A posterior oculardisease can include a disease, ailment, or condition, such asintraocular melanoma, acute macular neuroretinopathy, Behcet's disease,choroidal neovascularization, uveitis, diabetic uveitis, histoplasmosis,infections, such as fungal or viral-caused infections, maculardegeneration, such as acute macular degeneration, non-exudativeage-related macular degeneration and exudative age related maculardegeneration, edema, such as macular edema, cystoid macular edema anddiabetic macular edema, multifocal choroiditis, ocular trauma whichaffects a posterior ocular site or location, ocular tumors, retinaldisorders, such as central retinal vein occlusion, diabetic retinopathy(including proliferative diabetic retinopathy), proliferativevitreoretinopathy (PVR), retinal arterial occlusive disease, retinaldetachment, uveitic retinal disease, sympathetic opthalmia, VogtKoyanagi-Harada (VKH) syndrome, uveal diffusion, a posterior ocularcondition caused by or influenced by an ocular laser treatment,posterior ocular conditions caused by or influenced by a photodynamictherapy, photocoagulation, radiation retinopathy, epiretinal membranedisorders, branch retinal vein occlusion, anterior ischemic opticneuropathy, non-retinopathy diabetic retinal dysfunction, retinitispigmentosa, retinoblastoma, and glaucoma. Glaucoma can be considered aposterior ocular condition in some embodiments because the therapeuticgoal is to prevent the loss of or reduce the occurrence of loss ofvision due to damage to or loss of retinal cells or optic nerve cells(i.e., neuroprotection). In some embodiments, the present disclosureprovides a method to treat, or prevent glaucoma in a subject. In someembodiments, the present disclosure provides a method to treat, orprevent uveitis in a subject.

In some embodiments, the present disclosure provides a method to treator prevent dry eye in a subject. In some embodiments, the compositionsdescribed herein may address these issues by facilitating effectivedelivery of pharmaceutical agents to the appropriate tissues, promotingmore even and/or wide-spread coverage across the eye surface, and/oravoiding or minimizing clearance of the pharmaceutical agent.

In some embodiments, the present disclosure provides a method to treator prevent inflammation in the eye of a subject. Inflammation isassociated with a variety of ocular diseases. Inflammation may alsoresult from a number of ophthalmic surgical procedures, includingcataract surgery. Corticosteroids are often used as ocularanti-inflammatory agents, however, they typically require frequentdosing.

In some embodiments, the present disclosure provides a method to treator prevent age-related macular degeneration (AMD) in a subject. AMD is amedical condition that typically affects older adults and results in aloss of vision in the center of the visual field (the macula) because ofdamage to the retina. It occurs in “dry” and “wet” forms. It is a majorcause of blindness and visual impairment in older adults (>50 years). Inthe dry (nonexudative) form, cellular debris called drusen accumulatebetween the retina and the choroid, and the retina can become detached.In the wet (exudative) form, which is more severe, blood vessels grow upfrom the choroid behind the retina, and the retina can also becomedetached.

In certain embodiments, the compounds, particles, compositions, and/orformulations described herein are packaged as a ready to use shelfstable suspension. Eye drop formulations are traditionally liquidformulations (solutions or suspensions) which can be packaged in dropperbottles (which dispense a standard drop volume of liquid) or inindividual use droppers (typically used for preservative free drops,used once and disposed). These formulations are ready to use and can beself-administered. In some cases the bottle should be shaken before useto ensure homogeneity of the formulation, but no other preparation maybe necessary. This may be the simplest and most convenient method ofocular delivery. The compositions and/or formulations described hereincan be packaged in the same way as traditional eye drop formulations.

In some embodiments, compounds described here are useful in treating aproliferative disease, such as cancer, a benign neoplasm, an autoimmunedisease, or an inflammatory disease.

In some embodiments, a provided compound is useful in treating a cancer.In some embodiments, the present disclosure provides a method to treat acancer. In some embodiments, a provided compound is useful to delay theonset of, slow the progression of, or ameliorate the symptoms of cancer.In some embodiments, a provided compound is administered in combinationwith other compounds, drugs, or therapeutics to treat cancer.

In some embodiments, compounds described herein are useful for treatinga cancer including, but not limited to, acoustic neuroma,adenocarcinoma, adrenal gland cancer, anal cancer, angiosarcoma (e.g.,lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma),appendix cancer, benign monoclonal gammopathy, biliary cancer (e.g.,cholangiocarcinoma), bladder cancer, breast cancer (e.g., adenocarcinomaof the breast, papillary carcinoma of the breast, mammary cancer,medullary carcinoma of the breast), brain cancer (e.g., meningioma;glioma, e.g., astrocytoma, oligodendroglioma; medulloblastoma), bronchuscancer, carcinoid tumor, cervical cancer (e.g., cervicaladenocarcinoma), choriocarcinoma, chordoma, craniopharyngioma,colorectal cancer (e.g., colon cancer, rectal cancer, colorectaladenocarcinoma), epithelial carcinoma, ependymoma, endotheliosarcoma(e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma),endometrial cancer (e.g., uterine cancer, uterine sarcoma), esophagealcancer (e.g., adenocarcinoma of the esophagus, Barrett's adenocarinoma),Ewing sarcoma, eye cancer (e.g., intraocular melanoma, retinoblastoma),familiar hypereosinophilia, gall bladder cancer, gastric cancer (e.g.,stomach adenocarcinoma), gastrointestinal stromal tumor (GIST), head andneck cancer (e.g., head and neck squamous cell carcinoma, oral cancer(e.g., oral squamous cell carcinoma (OSCC), throat cancer (e.g.,laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer,oropharyngeal cancer)), hematopoietic cancers (e.g., leukemia such asacute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acutemyelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronicmyelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chroniclymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL); lymphoma suchas Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkinlymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma(DLCL) (e.g., diffuse large B-cell lymphoma (DLBCL)), follicularlymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma(CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas(e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodalmarginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma),primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacyticlymphoma (i.e., “Waldenstrom's macroglobulinemia”), hairy cell leukemia(HCL), immunoblastic large cell lymphoma, precursor B-lymphoblasticlymphoma and primary central nervous system (CNS) lymphoma; and T-cellNHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheralT-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g.,mycosis fungiodes, Sezary syndrome), angioimmunoblastic T-cell lymphoma,extranodal natural killer T-cell lymphoma, enteropathy type T-celllymphoma, subcutaneous panniculitis-like T-cell lymphoma, anaplasticlarge cell lymphoma); a mixture of one or more leukemia/lymphoma asdescribed above; and multiple myeloma (MM)), heavy chain disease (e.g.,alpha chain disease, gamma chain disease, mu chain disease),hemangioblastoma, inflammatory myofibroblastic tumors, immunocyticamyloidosis, kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor,renal cell carcinoma), liver cancer (e.g., hepatocellular cancer (HCC),malignant hepatoma), lung cancer (e.g., bronchogenic carcinoma, smallcell lung cancer (SCLC), non-small cell lung cancer (NSCLC),adenocarcinoma of the lung), leiomyosarcoma (LMS), mastocytosis (e.g.,systemic mastocytosis), myelodysplastic syndrome (MDS), mesothelioma,myeloproliferative disorder (MPD) (e.g., polycythemia Vera (PV),essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocyticleukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilicsyndrome (HES)), neuroblastoma, neurofibroma (e.g., neurofibromatosis(NF) type 1 or type 2, schwannomatosis), neuroendocrine cancer (e.g.,gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoidtumor), osteosarcoma, ovarian cancer (e.g., cystadenocarcinoma, ovarianembryonal carcinoma, ovarian adenocarcinoma), papillary adenocarcinoma,pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductalpapillary mucinous neoplasm (IPMN), islet cell tumors), penile cancer(e.g., Paget's disease of the penis and scrotum), pinealoma, primitiveneuroectodermal tumor (PNT), prostate cancer (e.g., prostateadenocarcinoma), rectal cancer, rhabdomyosarcoma, salivary gland cancer,skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA),melanoma, basal cell carcinoma (BCC)), small bowel cancer (e.g.,appendix cancer), soft tissue sarcoma (e.g., malignant fibroushistiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor(MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma), sebaceous glandcarcinoma, sweat gland carcinoma, synovioma, testicular cancer (e.g.,seminoma, testicular embryonal carcinoma), thyroid cancer (e.g.,papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC),medullary thyroid cancer), urethral cancer, vaginal cancer and vulvarcancer (e.g., Paget's disease of the vulva).

In some embodiments, a provided compound is useful in treating ametabolic disease, such as diabetes or obesity. In some embodiments, aprovided compound is useful to delay the onset of, slow the progressionof, or ameliorate the symptoms of, diabetes. In some embodiments, thediabetes is Type 1 diabetes. In some embodiments, the diabetes is Type 2diabetes. In some embodiments, a provided compound is useful to delaythe onset of, slow the progression of, or ameliorate the symptoms of,obesity. In some embodiments, a provided compound could be used incombination with other compounds, drugs, or therapeutics, such asmetformin and insulin, to treat diabetes and/or obesity.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. It should beunderstood that these examples are for illustrative purposes only andare not to be construed as limiting this invention in any manner.

Example 1 Synthesis of Compounds Under Scheme 1 Compound 100

Free phenol (1 equiv) and potassium carbonate (5 equiv) were suspendedin N,N-dimethylformamide. Benzyl bromide (1.1 equiv) was added dropwiseand the reaction stirred at 45° C. for 2 hours. The solvent wasevaporated and the remaining crust suspended in H₂O. The slurry wassonicated and the solid filtered. Filter cake was washed with H₂O andhexane, then dried under high vacuum. 100 was isolated as light brownsolid, yield=1.7 g (95%), m/z 300 (M+H)⁺.

Compounds 26 & 101

4-Amino-3-chlorophenol hydrochloride (1.1 to 1.5 equiv) was suspended inN,N-dimethylfomamide. The suspension was purged with nitrogen and sodiumhydride (2 equiv, 60% suspension in oil) was added followed by potassiumcarbonate (2 equiv). 100 (1 equiv) was added and the suspension waspurged with nitrogen again. The suspension was heated for 2 hours at100° C. in an oil bath. The solvent was evaporated. The residue wastreated with water and sonicated. The solid was filtered, washed withwater and hexane, then dried under high vacuum overnight. 26 wasisolated as purple solid, yield=1.42 g (98%), m/z=407 (M+H)⁺. Theprocess was repeated using 4-Chloro-6-methoxy-7-benzyloxyquinazoline (1equiv.) instead of 100. From this, 101 was isolated as off-white solid,yield=2.70 g (100%), m/z=408 (M+H)⁺.

Compounds 39, 27, 102, & 103

26 (1 equiv) was dissolved in dichloromethane. Triethylamine (4 equiv)was added and the solution was cooled to −78° C. Phosgene (1.1 equiv,15% solution in toluene) was added and the solution stirred for 30minutes at −78° C. It was warmed to room temperature over 30 minutes andstirred for 30 minutes at room temperature. Ar—NH₂ (3 equiv) was addedand the reaction stirred overnight. The solvent was evaporated and theresidue was suspended in diethyl ether. Ether was evaporated and thecrude residue again suspended in diethyl ether and sonicated. The solidwas filtered off and suspended in saturated aqueous sodium bicarbonate.The solid was filtered and washed with water and hexane, then driedunder high vacuum overnight. When Ar=A as described in Scheme 1 wasused, 39 was isolated as reddish-brown solid, yield=0.64 g (72%),m/z=559 (M+H)⁺, and when Ar=B as described in Scheme 1 was used, 27 wasisolated as reddish-brown solid, yield=0.86 g (92%), m/z=531 (M+H)⁺.

This process was repeated using 101 instead of 26. From this process,when Ar=A as described in Scheme 1 was used, 102 was isolated as yellowsolid, yield=1.57 g (85%), m/z=559 (M+H)⁺, and when Ar=B as described inScheme 1 was used, 103 was isolated as yellow solid, yield=1.72 g(100%), m/z=533 (M+H)⁺.

Compounds 40A, 28, 104, & 105

In separate processes, each of 39, 27, 102, and 103 (1 equiv) wasdissolved in methanol or methanol-tetrahydrofuran mixture (4:1).Palladium catalyst (20 or 50% weight, 10% on carbon) was added and thesolution was hydrogenated at 40-50 psi of hydrogen. The catalyst wasfiltered off on a pad of CELITE and the filtrate evaporated. Product wasprecipitated from hexane/dichloromethane (90:10) and filtered, thendried under high vacuum.

Alternatively, hydrogenation can be accomplished using hydrogen transferconditions. Benzyl protected urea (1 equiv) was dissolved intrifluoroacetic acid. Palladium catalyst (15% weight, 10% on carbon) wasadded. Triethylsilane was added drop wise over 1 hour and the solutionwas stirred for 2 hours. The catalyst was filtered off on a small CELITEpad and the solvent evaporated. The residue was partitioned betweenhexane and saturated sodium bicarbonate (1:1) and sonicated. The solidwas filtered, then dissolved in ethyl acetate-methanol (9:1). Thesolvent was evaporated to a small volume, then diethyl ether was addedand the suspension sonicated. Solid was filtered and dried under highvacuum. When 39 was used, 40A was isolated as brown solid, yield=0.32 g(90%), m/z=468 (M+H)⁺. When 102 was used, 104 was isolated as off-whitesolid by hydrogenolysis, yield=0.36 g (86%) or as yellow solid bytransfer hydrogenation, yield=1.24 g (99%), m/z=469 (M+H)⁺. When 27 wasused, 28 was isolated as copper brown powder, yield=0.63 g (94%),m/z=441 (M+H)⁺. When 103 was used, 105 was isolated as cream solid,yield=0.41 g (100%), m/z=443 (M+H)⁺.

Compounds 106, 30, 107, and 108

In separate processes, each of 40A, 28, 104, and 105 (1 equiv) wasdissolved in N,N-dimethylformamide. Potassium carbonate (3 equiv) wasadded followed by 1-bromo-3-chloropropane (3 equiv). The suspension wasstirred at 45° C. for 3 hours. The solvent was evaporated and theresidue was treated with aqueous sodium bicarbonate and sonicated. Theprecipitate was filtered off, washed with water and hexane. Theprecipitate was dissolved in ethyl acetate-methanol (4:1) and dried withmagnesium sulfate. The solvent was evaporated, then product wasdissolved in N,N-dimethylformamide. Potassium bromide (1.5 equiv) wasadded followed by potassium carbonate (5 equiv) and2-oxa-7-azaspiro[3.5]nonane oxalate (2 equiv). The suspension wasstirred at 85° C. for 4 hours. The solvent was evaporated and theresidue was suspended in aqueous sodium bicarbonate and sonicated.Precipitate was filtered and dried under high vacuum. Final purificationwas achieved through prep HPLC. When 40A was used, 106 was isolated asoff-white solid, yield=100 mg (63%), m/z=636 (M+H)⁺, ¹H-NMR (CDCl₃, 400MHz): δ 1.89 (4 h, m), 2.12 (2H, m), 2.34 (3H, s), 2.52 (2H, t), 4.01(3H, s), 4.24 (2H, t), 4.42 (4H, s), 6.49 (1H, d), 6.86 (1H, m), 6.99(1H, m), 7.14 (2H, d), 7.23 (1H, d), 7.31 (1H, s), 7.42, (1H, s), 7.49(1H, s), 7.88 (1H, d), 8.31 (1H, d), 8.50 (1H, d). When 104 was used,107 was isolated as white solid, yield=57 mg (38%), m/z=636 (M+H)⁺,¹H-NMR (CDCl₃, 400 MHz): δ 1.59 (4H, s), 1.89 (4 h, s), 2.12 (2H, m),2.34 (3H, s), 2.51 (2H, t), 4.05 (3H, s), 4.26 (2H, t), 4.42 (4H, s),6.85 (1H, m), 6.96 (2H, m), 7.21 (2H, dd), 7.33, (2H, s), 7.51 (1H, s),7.88 (1H, d), 8.32 (1H, d), 8.62 (1H, s). When 28 was used, 30 wasisolated as reddish-brown solid, yield=25 mg (10%), m/z=609 (M+1),¹H-NMR (CDCl₃, 400 MHz): δ 1.88 (4 h, m), 2.12 (2H, m), 2.36 (4H, bs),2.43 (3H, s), 2.52 (2H, t), 4.01 (3H, s), 4.24 (2H, t), 4.41 (4H, s),6.04 (1H, s), 6.50 (1H, d), 7.12 (1H, dd), 7.27, (1H, m), 7.42 (1H, s),7.49 (1H, s), 8.37 (1H, d), 8.50 (1H, d). When 105 was used, 108 wasisolated as gray solid, yield=10 mg (4%), m/z=610 (M+1), ¹H-NMR (CDCl₃,400 MHz): δ 1.60 (3H, s), 1.88 (4 h, m), 2.12 (2H, m), 2.43 (3H, s),2.51 (2H, t), 4.04 (3H, s), 4.26 (2H, t), 4.41 (4H, s), 6.01 (1H, s),7.20 (1H, dd), 7.32, (1H, s), 7.37 (1H, d), 7.50 (1H, s), 8.42 (1H, d),8.61 (1H, s).

Example 2 Preparation of Compound 106

Compound 110

A mixture of 109 (100.0 g, 601.68 mmol), benzyl bromide (79.0 mL, 649.81mmol) and potassium carbonate (249.0 g, 1.8 mol) inN,N-dimethylformamide (2000 mL) was heated to 40° C. overnight. Thesolution was cooled to room temperature, poured into ice water (1500 mL)and stirred for 1 h. The resultant solid was filtered and washed by H₂O(2×500 mL), dried to give 110 (148.8 g, yield=96.5%) as a white solid.

Compound 111

HNO₃ (60.9 mL) was added dropwise to a solution of 110 (148.8 g, 580.57mmol) in dichloromethane (2500 mL) at 0° C. The reaction mixture wasstirred for 20 min at 0° C. H₂SO₄ (47.2 mL) was added and the mixturewas stirred for another 45 min. Additional HNO₃ (41.5 mL) was addeddropwise over 20 min. The reaction mixture was poured into ice water(1500 mL) and stirred for 30 min. The organic phase was separated andwashed with water (4×1000 mL) and saturated NaHCO₃ (800 mL), dried overNa₂SO₄, and concentrated in vacuo. The residue was trituated three timeswith methanol (500 mL) at reflux. The solid was filtered and dried inhigh vacuum to give 111 (126.9 g, yield=72.5%) as a light yellow solid.

Compound 112

A suspension of 111 (70 g, 232.33 mmol), Fe (61.6 g, 929.32 mmol) andammonium acetate (89.1 g, 975.79 mmol) in a mixture of toluene/H₂O (1150mL/1150 mL) was stirred at 105° C. overnight. The mixture was cooled toroom temperature, diluted with ethyl acetate (1500 mL), stirred for 3 hat room temperature and filtered. The filtrate was washed with H₂O(2×500 mL) and brine (500 mL), then dried over Na₂SO₄. The solution wasconcentrated in vacuum to give 112 (63.8 g, yield=100%) as a light brownsolid.

Compound 113

To a solution of 112 (59.2 g, 218.21 mmol) in dimethoxyethane (1500 mL)was added sodium methoxide (47.1 g, 873 mmol). The reaction mixture wasstirred for 30 min under N₂. Ethyl formate was added and the mixture wasstirred overnight. The reaction mixture was diluted with H₂O (800 mL)and acidified to pH 7 with 1M HCl. The precipitate was filtered andwashed with water (2×300 mL), then dried under high vacuum to afford 113(38.9 g, yield=63.4%) as a brown solid.

Compound 114

POCl₃ (385 mL) was added to 113 (38.5 g, 136.86 mmol) and the mixturewas stirred for 6 h at reflux temperature. About 300 mL POCl₃ wasremoved by vacuum. The residue was carefully poured into ice water (600mL) and the pH was adjusted to 8 with saturated NaHCO₃. The solution wasstirred for 4 h. The solid was filtered and washed with water, thendried to give 114 (28.6 g, yield=69.7%) as a brown solid.

Compound 115

Compound 114 (16 g, 53.37 mmol) was dissolved in trifluoroacetic acid(100 mL) and MeSO₃H (6.1 mL, 93.94 mmol) was added in one portion. Thereaction mixture was stirred at reflux for 3 h and was then cooled toroom temperature. The solvent was evaporated and the pH of the residuewas adjusted to 7 with 2.5 N NaOH. The resultant solid was crushed intosmall pieces and the mixture was stirred vigorously for 2 h. The solidwas filtered and dried under high vacuum to afford 115 (11.3 g,yield=100%) as a light brown solid.

Compound 116

Compound 115 (36.5 g, 174.14 mmol), 1-bromo-3-chloropropane (123.5 mL)and K₂CO₃ (239.9 g, 1738.11 mmol) were suspended in N,N-dimethylformamide (1500 mL) and stirred at room temperature for 16 h. Thesuspension was filtered and the filtrate was concentrated. The residuewas diluted with ethyl acetate (1000 mL) and H₂O (1000 mL). The aqueousphase was extracted with ethyl acetate (500 mL×2) and the combinedorganic phase was washed with H₂O (1000 mL) and brine (500 mL×6), driedover Na₂SO₄ and concentrated in vacuum to give 116 (38.9 g, yield=78.1%)as a brown solid.

Compound 117

2-oxa-7-azaspiro[3.5]nonane (16.6 g, 129 mmol), K₂CO₃ (29.7 g, 215.2mmol) and NaI (9.7 g, 64.92 mmol) were added to a solution of 116 (12.3g, 42.9 mmol) in N,N-dimethyl formamide (1500 mL). The reaction wasstirred at 70° C. for 16 h under N₂. The reaction mixture was cooled toroom temperature and water (2 L) was added. After extraction with ethylacetate, the combined organic phase was washed with H₂O (2×500 mL),brine (6×300 ml) and dried over Na₂SO₄. The solution was concentrated invacuum to give a brown solid. The brown solid was stirred in a mixtureof hexanes/ethyl acetate (200 mL/4 mL) for 2 h, filtered and dried togive 117 (13.7 g, yield=84.6%) as a light brown solid.

Compound 118

Potassium tert-butoxide (4.7 g, 42 mmol) and 4-amino-3-chlorophenolhydrochloride (3.1 g, 16.8 mmol) were added to a solution of 117 (5.3 g,14 mmol) in dimethylacetamide (30 mL). The solution was stirred at 98°C. overnight under N₂. The reaction mixture was cooled to roomtemperature and poured into ice water (100 mL) when the reaction wascompleted. The solution was extracted with ethyl acetate (3×100 mL). Thecombined organic phase was washed by brine (5×100 mL), dried overNa₂SO₄, and concentrated to give a brown solid. The crude product waspurified by gel-silica (methanol:dichloromethane=1:20) to afford 118(4.4 g, yield=64.7%) as a brown solid.

Compound 106

A mixture of 2-fluoro-5-methylaniline (4.6 g, 36.8 mmol) and triethylamine (7.4 g, 73.6 mmol) in toluene (70 mL) was added dropwise to asolution of triphosgene (11.2 g, 40.5 mmol) in toluene (80 mL) at 0° C.The reaction was stirred for 3 h at room temperature and then 2 h at 80°C. Toluene was removed by concentration. To the resultant residue wasadded 118 (4.4 g, 9.1 mmol) in toluene (80 mL) and the reaction mixturewas stirred overnight at 70° C. The reaction mixture was then cooled toroom temperature and poured into ice water (100 mL) and stirred for 2 h.The solid was filtered and washed with H₂O (3×30 mL) and ethyl acetate(30 mL), then dried over Na₂SO₄ and concentrated to give 106 (2.9 g,yield=50.2%) as an off white solid. m/z 635.4 [M+H]⁺. ¹H-NMR (CDCl₃, 400MHz): δ 1.94 (4H, bs); 2.16 (2H, bs); 2.43 (9H, m); 4.01 (3H, s); 4.22(2H, t); 4.43 (4H, s); 6.48 (1H, d); 6.85 (1H, m); 6.95 (1H, dd); 7.12(1H, dd); 7.22 (1H, d); 7.34 (1H, s); 7.45 (4H, m); 7.89 (1H, m); 8.30(1H, d); 8.50 (1H, d).

Example 3 Preparation of Compound 9

Compound 1

To a solution of methyl vanillate (150 g, 0.82 mol) in dryN,N-dimethylformamide (DMF) (1200 mL) was added 1-bromo-3-chloropropane(259.6 g, 1.65 mol) and K₂CO₃ (341 g, 2.47 mol). The mixture was stirredat 50° C. overnight. The reaction mixture was poured into water (300 mL)filtered, the solid was washed with water (500 mL) then hexane (250 mL),and dried to give 209 g (yield=97.9%) of 1 as a white solid.

Compound 2

1 (160 g, 0.62 mol) was taken in acetic acid (1100 mL) and aceticanhydride (90 mL) was added. The solution was cooled to 0° C. and nitricacid (90 mL) was added. The reaction mixture was stirred for 10 minutesat room temperature, then heated to 50° C. for 5 h. The reaction mixturewas cooled and was diluted with ethyl acetate (5000 mL). The ethylacetate layer was washed with aq. NaHCO₃ (2000 mL) and concentrated toafford 180 g (yield=95.8%) of 2 as a yellow solid.

Compound 3

To a solution of 2 (170 g, 559 mmol) in ethyl acetate/methanol (1500 mL,3:1) was added wet Pd/C (10%/w, 17.0 g). The reaction was stirred underH₂ balloon at room temperature overnight. The reaction mixture wasfiltered through a pad of CELITE and the filtrate was concentrated togive 170 g (yield=100%) of 3 as a yellow solid.

Compound 4

To a solution of 3 (48 g, 175 mmol) in methanol (150 mL) was addedmethyl orthoformate (46.4 g, 438 mmol), ammonium acetate (33.7 g, 438mmol). The reaction mixture was stirred at reflux for 5 h. Water (200mL) was added to the reaction mixture to precipitate a crystallineproduct. The crystalline product was collected by filtration, washedwith water (200 mL) and methanol (50 mL), then dried under reducedpressure to give 44 g (yield=93.4%) of 4 as a white solid.

Compound 5

The mixture of 4 (75 g, 279 mmol) and POCl₃ (100 mL) in toluene (500 mL)was stirred at reflux until the solution became clear. The solution wasconcentrated under reduced pressure and the residue was poured into icewater. After filtration, the solid was washed with water (500 mL×2) anddried to give 65 g (yield=81.2%) of 5 as a yellow solid.

Compound 6

The mixture of 5 (5 g, 17.4 mmol), 4-amino-3-chlorophenol-HCl (5.33 g,29.6 mmol), and Cs₂CO₃ (17 g, 52.3 mmol) in THF (60 mL) was stirred at50° C. overnight. The reaction mixture was diluted with ethyl acetate,and the ethyl acetate layer was washed with water (50 mL×1) and brine(50 mL×1) successively. The organic layer was dried with Na₂SO₄ andconcentrated to dryness. The residue was purified by silica column(petroleum ether:ethyl acetate=10:1 to 2:1) to give 4.6 g (yield=67%) of6 as a pink solid.

Compound 7

To the solution of triphosgene in toluene (30 mL) was added the mixtureof 3-amino-5-methylisoxazole (4.85 g, 49.5 mmol) and triethyl amine (10g, 99 mmol) in toluene (20 mL) dropwise at 0° C. The reaction mixturewas stirred at room temperature for 3 h then 80° C. for 2 h. Thereaction solution was concentrated in vacuum to give 7 as a white solid.

Compound 8

Compound 7 was dissolved in toluene (50 mL) and 6 (13 g, 33 mmol) wasadded. The mixture was heated to 70° C. for 4 h. The reaction mixturewas poured into ice water (100 mL) and extracted with ethyl acetate (200mL×2). The organic phase was washed with brine (100 mL×4), dried oversodium sulfate and concentrated. The residue was purified by silicacolumn (petroleum ether:ethyl acetate=5:1 to 1:1) to give 15 g(purity=80%, yield=87.8%) of 8 as a pink solid.

Compound 9

To the solution of 8 (15 g, 29 mmol, 80% pure) in N,N-dimethyl formamide(120 mL) was added 2-oxa-7-azaspiro[3.5]nonane hemioxalate (9.19 g, 72.4mmol), tetrabutyl ammonium iodide (10.69 g, 29 mmol), anddiisopropylethylamine (11.2 g, 86.9 mmol). The mixture was heated to 60°C. overnight. The reaction solution was diluted with ethyl acetate (200mL) and washed with brine (100 mL×5). The combined organic phase wasdried over sodium sulfate and concentrated to give the crude product asa black solid. The crude product was purified by silica column(dichloromethane:methanol=50:1 to 10:1) to give 5.1 g (yield=28.9%) of 9as a pink solid. m/z 609.4 [M+H]⁺. ¹H-NMR (DMSO-d6, 400 MHz): δ 1.75(4H, s); 1.92 (2H, m); 2.26 (4H; m); 2.26 (5H, s); 3.95 (3H, s); 4.10(6H, m); 6.50 (1H, s); 7.29 (2H, m); 7.31 (2H, m); 8.17 (1H, d); 8.54(1H, s); 8.74 (1H, s); 10.16 (1H, s).

Example 4 Preparation of Compound 12

Compound 10

To a solution of triphosgene in toluene (30 mL) was added the mixture of2-fluoro-5-methylaniline (4.76 g, 38.07 mmol) and triethylamine (7.69 g,76.14 mmol) in toluene (20 mL) dropwise at 0° C. The reaction mixturewas stirred at room temperature for 3 h then at 80° C. for 2 h. Thereaction solution was concentrated under vacuum to give the crudeproduct 10 as a white solid.

Compound 11

Compound 10 was dissolved in toluene (50 mL) and 6 (10 g, 25.38 mmol)was added. The mixture was heated to 70° C. for 4 h. The reactionmixture was poured into ice water and extracted with ethyl acetate (200mL×2). The organic phases were combined, washed with brine (100 mL×4),dried over sodium sulfate and concentrated. The residue was purified bysilica column (petroleum ether:ethyl acetate=2:1) to give 12 g(purity=80%, yield=86.8%) of 11 as a pink solid.

Compound 12

To a solution of 11 (15 g, 27.5 mmol, 80% pure) in N,N-dimethylformamide (120 mL) was added 2-oxa-7-azaspiro[3.5]nonane hemioxalate(9.10 g, 71.56 mmol), tetrabutylammonium iodide (10.16 g, 27.52 mmol),and diisopropylethyl amine (10.65 g, 82.57 mmol). The mixture was heatedto 60° C. overnight. The reaction solution diluted with ethyl acetate(200 mL) and washed with brine (100 mL×5), concentrated to give thecrude product as a black solid. The crude product was purified by silicacolumn (dichloromethane:methanol=50:1 to 10:1) to give 5.3 g(yield=30.3%) of 12 as a pink solid. m/z 636.4 [M+H]⁺. ¹H-NMR (CDCl₃,400 MHz): δ 1.25 (2H, s); 2.01 (4H, bs); 2.20 (5H, m); 2.68 (4H, m);4.03 (3H, s); 4.23 (2H, t); 4.44 (4H, s); 6.81 (1H, m); 6.92 (1H, dd);7.19 (1H, dd); 7.32 (2H, m); 7.44 (1H, m); 7.52 (2H, m); 7.91 (1H, d);8.31 (1H, d); 8.59 (1H, s).

Example 5 Preparation of Compound 14

Compound 13

To a solution of 6 (17.30 g, 43.91 mmol) in N,N-dimethylformamide (150mL) was added 2-oxa-7-azaspiro[3.5]nonane hemioxalate (11.15 g, 87.82mmol), tetrabutylammonium iodide (16.20 g, 43.91 mmol) and DIPEA (16.99g, 131.73 mmol). The reaction mixture was heated to 60° C. and stirredovernight. The reaction mixture was diluted with ethyl acetate (200 mL)and washed with brine (100 mL×5). The organic phase was concentrated togive the crude product as a black solid. The crude product was purifiedby silica column (dichloromethane:methanol=50:1 to 10:1) to give 15 g(yield=70.4%) of 13 as a light brown solid.

Compound 14

1,3-Dimethyl-1H-pyrazole-5-carboxylic acid acid (0.10 g, 0.69 mmol) wassuspended in dichloromethane (3 mL). Oxalyl chloride (0.25 mL, 2.9 mmol)was added followed by catalytic amount of N,N-dimethylformamide (1drop). The solution was stirred for 2 h. The solvent was removed and theresidue was re-dissolved in dichloromethane (5 mL). The solvent wasagain removed leaving an oil. The material was dissolved indichloromethane (3 mL) and added to the solution of aniline 13 (0.24 g,0.5 mmol) and triethylamine (0.15 mL, 1.0 mmol) in tetrahydrofuran (5mL). The solution was stirred for 2 h and then partitioned between ethylacetate and aqueous sodium bicarbonate. The organic solution was driedwith magnesium sulfate and evaporated leaving an oil (0.4 g).Purification was performed using reverse phase flash chromatography toyield 14 as off white solid (84 mg) m/z: 607.2 [M+H]⁺. ¹H NMR:(DMSO-d6): δ 10.02 (s, 1H), 8.58 (s, 1H), 7.66-7.61 (m, 2H), 7.55 (s,1H), 7.40-7.38 (m, 2H), 6.86 (s, 1H), 4.27 (s, 4H), 4.23 (t, J=6.5 Hz,2H), 4.01 (s, 3H), 3.98 (s, 3H), 2.40 (t, J=6.5 Hz, 2H), 2.34-2.18 (m,4H), 2.21 (s, 3H), 1.99-1.93 (m, 2H), 1.82-1.70 (m, 4H).

Example 6 Preparation of Compound 15

Compound 15

Triethylamine (1.12 mL, 8 mmol) was added to a solution of 13 (970 mg, 2mmol) in dichloromethane and cooled to −78° C. Phosgene (15% solution intoluene, 1.45 mL, 2.2 mmol) was added dropwise and the reaction stirredfor 30 minutes at −78° C., then at room temperature for 30 minutes. Asolution of 4-chloro-3-(trifluoromethyl)aniline (1.17 g, 6 mmol) indichloromethane was added dropwise and the reaction stirred overnight. Asmall amount of methanol was added and the solvent evaporated by rotaryevaporator. dichloromethane was added and the solvent evaporated again.Crude product was precipitated from diethylether orhexane/dichloromethane and filtered. Final purification was achieved byprep LC to yield 79 mg (0.11 mmol, Yield=6%) of 15 as a white solid.m/z: 706.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ 1.77 (6H, t); 1.96 (3H, m);2.40 (4H, t); 3.97 (5H, s); 4.22 (3H, t); 4.27 (7H, s); 7.30 (1H, dd);7.37 (1H, s); 7.54 (1H, s); 7.56 (1H, d); 7.64 (3H, m); 8.15 (3H, m);8.56 (1H, s).

Example 7 Preparation of Compound 16

Compound 16

Triethylamine (1.15 mL, 8.24 mmol) was added to a solution of 13 (1 g,2.06 mmol) in dichloromethane and cooled to −78° C. Phosgene (15%solution in toluene, 3 mL, 4.52 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. 3-aminothiophene (612 mg, 6.18 mmol) in dichloromethane (2mL) was added dropwise and the reaction stirred overnight. A smallamount of methanol was added and the solvent evaporated by rotaryevaporator. dichloromethane was added and the solvent evaporated again.Crude product was precipitated from diethylether/dichloromethane andfiltered to yield pink solid. 1.25 g crude was suspended in saturatedaqueous NaHCO₃ and extracted with 10% methanol/dichloromethane. Organicswere dried over MgSO₄, filtered, and evaporated by rotary evaporation.Remaining solid was dissolved in ethyl acetate (10 mL) and sonicated toinduce crystallization. Crystalline product was filtered and dried underhigh vacuum overnight to give 325 mg (Yield=6.47%) of 16 as a tanpowder. m/z 610.2 [M]. ¹H-NMR (DMSO-d6, 400 MHz): δ 1.77 (4H, t); 1.96(2H, m); 2.28 (4H, bs); 2.41 (2H, t); 3.97 (3H, s); 4.22 (2H, t); 4.27(4H, s); 5.76 (1H, s); 7.05 (1H, d); 7.31 (2H, m); 7.36 (1H, s); 7.47(1H, dd); 7.54 (2H, s); 8.23 (1H, d); 8.33 (1H, s); 9.68 (1H, s).

Example 8 Preparation of Compound 17

Compound 17

Triethylamine (1.15 mL, 8.24 mmol) was added to a solution of 13 (1 g,2.06 mmol) in dichloromethane and cooled to −78° C. Phosgene (15%solution in toluene, 3 mL, 4.52 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. Propylamine (508 μL, 6.18 mmol) in DCM (2 mL) was addeddropwise and the reaction stirred overnight. A small amount of methanolwas added and the solvent evaporated by rotary evaporator.Dichloromethane was added and the solvent evaporated again. Crudeproduct was precipitated from 10:1 hexane/dichloromethane and filtered.Crude was suspended in saturated aqueous NaHCO₃ and extracted with 10%methanol/dichloromethane. Organics were dried over MgSO₄, filtered, andevaporated by rotary evaporation. Remaining solid was dissolved in ethylacetate (10 mL) and sonicated to induce crystallization. Crystallineproduct was filtered and dried under high vacuum overnight to give 900mg (1.58 mmol, Yield=77%) of 17 as off-white solid. m/z 570.3 [M].¹H-NMR (DMSO-d6, 400 MHz): δ 0.89 (3H, t); 1.45 (2H, q); 1.76 (4H, m);1.94 (2H, m); 3.06 (2H, q); 3.95 (3H, s); 4.20 (2H, t); 4.22 (4H, s);5.74 (1H, s); 6.98 (1H, t); 7.20 (1H, dd); 7.35 (1H, s); 7.45 (1H, d);7.52 (1H, s); 8.03 (1H, s); 8.19 (1H, d); 8.53 (1H, s).

Example 9 Preparation of Compound 126(4-Chloro-6-Methoxy-Quinazolin-7-ol)

Compound 119

A mixture of methyl vanillate (300.0 g, 1.65 mol), benzyl chloride (230mL, 1.81 mol) and potassium carbonate (345 g, 2.5 mol) in N,N-dimethylformamide (1000 mL) was heated to 100° C. for three hours. The reactionwas cooled to room temperature, poured into ice water (1500 mL) andstirred for 1 h. The resultant solid was filtered and washed by water(300 mL×3), then dried to give 119 (440 g, yield=98.0%) as a whitesolid.

Compound 120

A mixture of HNO₃ (95%, 1000 mL) and acetic acid (1000 mL) was placed inan ice bath and stirred. Compound 119 (440 g, 1.62 mol) in acetic acid(2500 mL) was added dropwise at −10° C. After addition, the mixture wasstirred at −10° C. for 20 min, then poured onto a mixture of ice andwater (2 L). The mixture was neutralized by the addition of saturatedaqueous sodium hydroxide solution to pH 7 and solid precipitated out.The precipitate was collected by filtration, washed with water (300mL×3) and dried to yield 120 (495 g, yield 97.1%) as a grey solid.

Compound 121

A suspension of 120 (495 g, 1.56 mol), Fe (305.7 g, 5.46 mol) and NH₄Cl(337.0 g, 6.24 mol) in a mixture of methanol/H₂O (1500 mL/500 mL) wasstirred at 105° C. overnight. The mixture was cooled to roomtemperature, diluted with ethyl acetate (1500 mL), stirred for 3 h atroom temperature and filtered. The filtrate was washed with water (500mL×3) and brine (500 mL×3), then dried over Na₂SO₄. The solution wasconcentrated in vacuum to give 121 (363.8 g, yield=81%) as a light brownsolid.

Compound 122

In a 3 L volume stainless pressure-resistant vessel equipped with astirrer, a thermometer and a pressure gauge were placed 121 (363.8 g,1.267 mol), methyl orthoformate (336.0 g, 3.167 mol), ammonium acetate(243.9 g, 3.167 mol), and methanol (1500 mL). The vessel was closed, andthe reaction was carried out at 100° C. overnight. After the reactionwas complete, water (1500 mL) was added to the reaction mixture. Themixture was stirred at 0-10° C. for 1 hour to generate a crystallineproduct. The crystalline product was collected by filtration, washedwith water (300 mL×3), and dried to give 122 (247 g, yield=69%) as palesolid.

Compound 123

Compound 122 (247 g, 875.6 mmol) was dissolved in trifluoroacetic acid(800 mL), and CH₃SO₃H (127 mL) was added in one portion. The reactionwas heated to reflux for 3 h, then cooled to room temperature andconcentrated. Aqueous 2.5 N NaOH was added to adjust the pH of thesolution to 7, which caused precipitation. The resultant solid wascrushed, was stirred vigorously for 1 h, and was then filtered. Thesolid was collected and dried under high vacuum to afford 123 (148 g,yield=88%) as brown solid.

Compound 124

Pyridine (145 ml) was added to a suspension of 123 (148 g, 770.15 mmol)in acetic anhydride (800 ml). The reaction mixture was heated to 120° C.for 3 h, during which time the solid dissolved. The reaction mixture wasallowed to cool, then poured into ice-water. The reaction mixture wasstirred for 1 h, then the solid was removed by filtration and dried overto give 124 (100 g, yield=55.4%) as brown solid.

Compound 125

N,N-dimethylformamide (1 mL, cat.) was added to a solution of 124 (100g, 426.97 mmol) in SOCl₂ (300 mL) and the reaction mixture was heated toreflux for 1.5 h. Upon cooling to room temperature, the SOCl₂ wasremoved in vacuo and azeotroped with toluene (100 mL×3) to give 125.

Compound 126 (4-Chloro-6-Methoxy-Quuinazoline-7-ol)

Residue 125 was diluted with dichloromethane, a solution of 10%NH₃/methanol was added, and the mixture heated at 80° C. for 10 minutes.Upon cooling to room temperature, the solvent was removed, water wasadded and the pH of the mixture was adjusted to 7 with HCl (4 N). Theresultant precipitate was collected by filtration and dried in vacuo togive 126, 4-chloro-6-methoxy-quinazolin-7-ol (47 g, two steps,yield=52.3%) as a pale solid.

Example 10 Preparation of Compound 21

Compound 18

To a solution of 2-oxa-7-azaspiro[3.5]nonane hemioxalate (18.6 g, 146.46mmol) in acetonitrile (200 mL) was added 3-chloropropan-1-ol (20.76 g,219.69 mmol), potassium carbonate (40.42 g, 292.91 mmol), and potassiumiodide (24.31 g, 146.46 mmol). The mixture was heated to reflux andstirred overnight. The reaction solution was diluted with ethyl acetate(200 mL) and filtered to remove the solid. The filtrate was concentratedto dryness and the residue was dissolved in water and lyophilized todryness to give 18 (17 g, Yield=62.7%) as a yellow oil.

Compound 19

4-Chloro-6-methoxy-quinazolin-7-ol (9.5 g, 45.11 mmol), 18 (10.03 g,54.13 mmol), and triphenylphosphine (23.73 g, 90.22 mmol) were stirredin tetrahydrofuran (300 mL) and cooled in an ice bath. Dibenzylazodicarboxylate (20.75 g, 90.22 mmol) in tetrahydrofuran (80 mL) wasadded dropwise. The reaction mixture stirred at room temperature. for 2h. The reaction solution was diluted with ethyl acetate (300 mL), washedwith water (200 mL×2). The organic phase concentrated to give the crudeproduct as a brown oil. Column chromatography of the crude product gave19 (5.1 g, Yield=29.9%) as a yellow solid.

Compound 20

1,3-Dimethyl-1H-pyrazole-5-carboxylic acid (0.70 g, 5.0 mmol) wassuspended in dichloromethane (10 mL). Oxalyl chloride (1.0 mL, 11.6mmol) was added followed by catalytic amount of N,N-dimethylformamide (1drop). The solution was stirred for 2 h. The solvent was removed and theresidue was re-dissolved in dichloromethane (10 mL). The solvent wasagain removed leaving an oil. The material was dissolved indichloromethane (5 mL) and added to the solution of4-amino-3-methylphenol (0.62 g, 5.0 mmol) and triethylamine (1.0 mL, 7.0mmol) in tetrahydrofuran (30 mL). The solution was stirred for 3 h andthen evaporated. The residue was treated with aqueous sodiumbicarbonate. The solid was filtered off and washed with water. Drying inhigh vacuum afforded 20 as an off white solid (1.20 g).

Compound 21

Compound 19 (0.38 g, 1.0 mmol),N-(4-hydroxy-2-methylphenyl)-1,3-dimethyl-1H-pyrazole-5-carboxamide(0.25 g, 1.0 mmol) and potassium carbonate (0.41 g, 3.0 mmol) weresuspended in N,N-dimethylformamide (5 mL). The solution was heated to90° C. for 4 h. The solvent was evaporated and the residue was dilutedwith water. The solid was filtered off and dried in high vacuum.Purification by reverse phase flash chromatography gave 21 as off whitesolid 038 mg) m/z: 587.3 [M+H]⁺. ¹H NMR: (DMSO-d6): δ 9.81 (s, 1H), 8.55(s, 1H), 7.66-7.61 (m, 2H), 7.55 (s, 1H), 7.39 (d, J=8.5 Hz, 1H), 7.36(s, 1H), 7.24 (d, J=2.5 Hz, 1H), 7.16 (dd, J=8.5 Hz, 2.5 Hz, 1H), 6.83(s, 1H), 4.27 (s, 4H), 4.22 (t, J=6.5 Hz, 2H), 4.01 (s, 3H), 3.98 (s,3H), 2.41 (t, J=6.5 Hz, 2H), 2.33-2.21 (m, 4H), 2.25 (s, 3H), 2.21 (s,3H), 1.99-1.93 (m, 2H), 1.80-1.70 (m, 4H).

Example 11 Preparation of Compound 25

Compound 22

Compound 126 of Example 9 (36.5 g, 174.14 mmol), 1-bromo-3-chloropropane(123.5 mL) and potassium carbonate (239.9 g, 1738.11 mmol) weresuspended in N,N-dimethylformamide (1500 mL) and stirred at roomtemperature for 16 h. The suspension was filtered and the filtrate wasconcentrated. The residue was diluted with ethyl acetate (1000 mL) andwater (1000 mL). The aqueous phase was extracted with ethyl acetate (500mL×2) and the combined organic phase was washed with water (1000 mL) andbrine (500 mL×6), dried over Na₂SO₄ and concentrated in vacuum to give22 (38.9 g, Yield=78.1%) as a brown solid.

Compound 23

2-oxa-7-azaspiro[3.5]nonane (16.6 g, 129 mmol), potassium carbonate(29.7 g, 215.2 mmol) and sodium iodide (9.7 g, 64.92 mmol) were added toa solution of 22 (12.3 g, 42.9 mmol) in N,N-dimethylformamide (1500 mL),stirred at 70° C. for 16 h under N₂. The reaction mixture was cooled toroom temperature and water (2 L) was added. After extracted with ethylacetate, the combined organic phase was washed with water (500 mL×2),brine (300 ml×6) and dried over Na₂SO₄. The solution was concentrated invacuum to give a brown solid. The brown solid was stirred in a mixtureof hexane/ethyl acetate (200 mL/4 mL) for 2 h, filtered and dried togive 23 (13.7 g, Yield=84.6%) as a light brown solid.

Compound 24

Potassium tert-butoxide (4.7 g, 42 mmol) and 4-amino-3-chlorophenol-HCl(3.1 g, 16.8 mmol) were added to a solution of 23 (5.3 g, 14 mmol) inDMA (30 mL). The solution was stirred at 98° C. overnight under N₂.Cooled to room temperature and poured into ice water (100 mL) when thereaction was completed. The solution was extracted with ethyl acetate(100 mL×3). The combined organic phase was washed by brine (100 mL×5),dried over Na₂SO₄, and concentrated to give a brown solid. The crudeproduct was purified by gel-silica (methanol:dichloromethane=1:20) toafford 24 (4.4 g, Yield=64.7%) as a brown solid.

Compound 25

A mixture of 2-fluoro-5-methylaniline (4.6 g, 36.8 mmol) andtriethylamine (7.4 g, 73.6 mmol) which was dissolved in toluene (70 mL)was added dropwise to a solution of triphosgene (11.2 g, 40.5 mmol) intoluene (80 mL) at 0° C. Then the reaction was stirred for 3 h at roomtemperature and then 2 h at 80° C. Toluene was removed by concentrated.To the resultant residue was added 24 (4.4 g, 9.1 mmol) in toluene (80mL) and the reaction mixture was stirred overnight at 70° C. Thereaction mixture was then cooled to room temperature. and poured intoice water (100 mL) and stirred for 2 h. The solid was filtered andwashed with water (30 mL×3) and ethyl acetate (30 mL), dried in Na2SO4,and concentrated to give 25 (2.9 g, Yield=50.2%) as an off-white solid.m/z 635.4 [M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 1.94 (4H, bs); 2.16 (2H,bs); 2.43 (9H, m); 4.01 (3H, s); 4.22 (2H, t); 4.43 (4H, s); 6.48 (1H,d); 6.85 (1H, m); 6.95 (1H, dd); 7.12 (1H, dd); 7.22 (1H, d); 7.34 (1H,s); 7.45 (4H, m); 7.89 (1H, m); 8.30 (1H, d); 8.50 (1H, d).

Example 12 Preparation of Compound 30

Compound 26

A solution of 4-amino-3-chlorophenol HCl (828 mg, 4.6 mmol) and sodiumhydride (60% dispersion in mineral oil, 368 mg, 9.2 mmol) in dryN,N-dimethylformamide (10 mL) was sparged with N₂. Potassium carbonate(1.27 g, 9.2 mmol) was added, followed by7-benzyloxy-4-chloro-6-methoxy-quinoline (932 mg, 3.12 mmol). Thereaction was stirred at 100° C. for 17 h, then cooled to roomtemperature and the solvent removed by rotary evaporator. Crude residuewas suspended in water and extracted with ethyl acetate (100 mL×4). Thecombined organics were dried over MgSO₄, filtered, and the solventevaporated. Final product was precipitated from water, filtered, anddried under high vacuum to yield 1.37 g (3.37 mmol, Yield=93%) of 26 aspurple solid.

Compound 27

A solution of 26 (712 mg, 1.75 mmol) and triethylamine (978 μL, 7.01mmol) in dichloromethane (20 mL) was cooled to −78° C. Phosgene (15% intoluene, 1.27 mL, 1.93 mmol) was added dropwise and the reaction stirredfor 30 minutes, then at room temperature for 30 minutes. A solution of3-amino-5-methyl isoxazole (516 mg, 5.26 mmol) in dichloromethane (10mL) was added dropwise and the reaction stirred overnight. The solventwas removed by rotary evaporator and the crude co-evaporated withdiethyl ether (50 mL). Product was precipitated from diethyl ether andfiltered, then suspended in saturated aqueous sodium bicarbonate andfiltered. The product was dried under high vacuum to yield 937 mg (1.75mmol, Yield=99%) of 27 as a chocolate brown powder.

Compound 28

Compound 27 (806 mg, 1.52 mmol) was dissolved in methanol (200 mL) and100 mL loaded into a Parr vessel. Palladium hydroxide (200 mg, 50%weight) was added and the reaction agitated under 50 psi of H₂. Reactionwas stopped after 2 h and the slurry filtered through CELITE. Filtratewas evaporated, then co-evaporated with dichloromethane (50 mL) anddiethyl ether (50 mL) respectively. Product was precipitated from 10:1hexane/dichloromethane, filtered, and dried under high vacuum. Afterrepeating procedure with remaining starting material, 625 mg (1.42 mmol,Yield=93%) of 28 was isolated as copper brown solid.

Compound 29

Compound 28 (310 mg, 0.7 mmol) and potassium carbonate (292 mg, 2.11mmol) were suspended in dry N,N-dimethylformamide (5 mL).1-bromo-3-chloropropane (208 μL, 2.11 mmol) was added dropwise and thereaction stirred at 50° C. for 2 h. The solvent was removed by rotaryevaporator and the crude residue partitioned between saturated aqueoussodium bicarbonate and ethyl acetate. The organics were separated, driedover MgSO₄, filtered, and the solvent evaporated. The product residuewas loaded onto a silica plug and washed first with dichloromethane (60mL) followed by 20% methanol/ethyl acetate (120 mL). Product wasrecovered from the methanol/ethyl acetate fraction and the solventevaporated. 29 was co-evaporated with dichloromethane and used in thenext reaction without further purification.

Compound 30

Compound 29 (210 mg, 0.41 mmol), potassium carbonate (280 mg, 2.03mmol), and potassium bromide (97 mg, 0.81 mmol) were suspended in dryN,N-dimethylformamide (5 mL). 2-Oxa-7-azaspiro[3.5]nonane hemioxalatewas added and the reaction stirred at 80° C. for 5 h. Solvent wasremoved by rotary evaporator and the crude residue partitioned betweensaturated aqueous sodium bicarbonate and 10% methanol/ethyl acetate. Theorganics were separated, dried over MgSO₄, filtered, and the solventevaporated. Residue was co-evaporated with dichloromethane (50 mL×2) andthe crude product dried under high vacuum. Final purification wasachieved by prep LC. 6 mg (0.01 mmol, Yield=2%) of light brown powder 30was isolated. m/z 608.2 [M]. ¹H-NMR (CDCl₃, 400 MHz): δ 1.89 (4H, m);2.12 (2H, m); 2.43 (3H, s); 2.53 (2H, t); 4.02 (3H, s); 4.25 (2H, t);4.42 (4H, s); 6.04 (1H, bs); 6.50 (1H, d); 7.14 (1H, dd); 7.26 (1H, s);7.42 (1H, s); 7.49 (1H, s); 8.38 (1H, d); 8.50 (1H, d).

Example 13 Preparation Compound 35

Compound 31

To a solution of 126 of Example 9 (3.0 g, 14.25 mmol) andethyl-4-bromobutyrate (4.53 g, 28.49 mmol) in tetrahydrofuran (30 mL)was added K₂CO₃ (5.90 g, 42.74 mmol). The mixture was stirred at roomtemperature overnight. The reaction mixture was diluted with water (60mL) and extracted with ethyl acetate (100 mL×2). The combined organicphase was concentrated to give the crude product as a yellow solid.Thecrude product was purified by silica gel column (hexanes:ethylacetate=10:1 to 2:1) to give 3.7 g (yield=80%) of 31 as a yellow solid.

Compound 32

To a solution of 31 (2 g, 6.16 mmol) and 4-amino-3-chlorophenol-HCl(1.55 g, 8.62 mmol) in acetonitrile (20 mL) was added Cs₂CO₃ (6.02 g,18.47 mmol). The mixture was stirred at 50° C. for 2 h. TLC showed that31 was consumed. The solid was removed by filtration and the filtratewas concentrated under vacuum to give a brown solid. The brown solid wasdissolved in ethyl acetate (50 mL) and washed with water (50 mL×2). Theorganic phase was concentrated and the residue was purified by silicacolumn (hexanes:ethyl acetate=5:1 to 1:1) to give 1.7 g (yield=63.9%) of32 as a purple solid.

Compound 33

A solution of 32 (6.00 g, 13.89 mmol) and 10 (6.00 g, crude) indichloromethane (200 mL) was stirred at room temperature for 4 h. Thereaction mixture was washed with water (100 mL×2). The organic layer wasconcentrated under vacuum to give a residue, which was purified bysilica column (dichloromethane to dichloromethane:methanol=25:1) to give6.50 g (yield=84.2%) of 33 as a purple solid.

Compound 34

To a solution of 33 (8.60 g, 15.47 mmol) in tetrahydrofuran (400 mL) wasadded aqueous LiOH solution (1.0 N, 77.34 mL) dropwise. The reactionmixture was stirred at room temperature overnight. The reaction mixturewas concentrated to dryness to give 9.6 g of crude product 34 as a brownsolid. The crude product was used directly in the next step withoutfurther purification.

Compound 35

To a solution of 34 (400 mg, 0.76 mmol) in N,N-dimethylformamide (5 mL)was added 1-hydroxybenzotriazole (204 mg, 1.52 mmol), 12 (144 mg, 1.14mmol), diisopropylethyl amine (293 mg, 2.27 mmol) andN-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (290 mg,1.52 mmol) sequentially. The reaction mixture was stirred at roomtemperature overnight. The reaction mixture was poured into water (50mL) and grey solid precipitated out. The solid was collected byfiltration. This solid was purified by silica column (dichloromethane todichloromethane:methanol=10:1) to give a pink solid. This pink solid wasdissolved in 5 mL of dichloromethane:methanol (5:1). Dichloromethane wasremoved under vacuum and a pink solid precipitated out from methanol.The pink solid was collected by filtration to give 200 mg (yield=41.4%)of 35. m/z 637.4 [M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 1.72 (4H, m); 2.28(2H, t); 2.42 (3H, s); 2.60 (2H, t); 4.04 (3H, s); 4.27 (2H, t); 4.29(4H, q); 6.01 (1H, s); 7.18 (1H, dd); 7.34 (2H, s); 7.50 (1H, s); 8.40(1H, d); 8.62 (2H, s)

Example 14 Preparation of Compound 38

Compound 36

A mixture of 32 (900 mg, 2.08 mmol) and 10 (900 mg, crude) in toluene(15 mL) was stirred at 70° C. for 3 h. The reaction mixture wasconcentrated under vacuum to give a residue. The residue was dilutedwith dichloromethane (50 mL) and washed with water (50 mL×2). Theorganic layer was concentrated and the residue was purified by silicacolumn (dichloromethane:methanol=50:1 to 10:1) to give 1.15 g(yield=94.7%) of 36 as a purple solid.

Compound 37

To a solution of 36 (1.15 g, 1.97 mmol) in tetrahydrofuran (55 mL) wasadded aqueous LiOH solution (1N, 13.31 mL) dropwise. The reactionmixture was stirred at room temperature overnight. The reaction solutionwas concentrated to dryness to give 9.6 g of the crude product 37 as abrown solid. The crude product was used directly for the next stepwithout further purification.

Compound 38

To the solution of 37 (1.20 g, 2.16 mmol) in N,N-dimethylformamide (12mL) was added 1-hydroxybenzotriazole (580 mg, 4.32 mmol),2-oxa-7-azaspiro[3.5]nonane (410 mg, 3.24 mmol), diisopropylethylamine(840 mg, 6.49 mmol) and N-(3-dimethylaminopropyl)-N′-ethylcarbodiimidehydrochloride (830 mg, 4.32 mmol) sequentially. The reaction mixture wasstirred at room temperature overnight and then was poured into water(100 mL). Gray solid precipitated out and was collected by filtration.This solid was purified by silica column (dichloromethane todichloromethane:methanol=10:1) to give 1.07 g (yield=74.5%) of 38 as apink solid. m/z 664.4 [M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 1.83 (4H, dt);2.10 (2H, m); 2.29 (3H, s); 2.61 (2H, t); 3.42 (2H, t); 3.54 (2H, t);4.03 (3H, s); 4.27 (2H, t); 4.45 (4H, q); 6.85 (1H, m); 6.95 (1H, m);6.99 (1H, s); 7.17 (1H, dd); 7.29 (2H, d); 7.36 (1H, s); 7.50 (1H, s);7.89 (1H, m); 8.32 (1H, d); 8.62 (1H, s).

Example 15 Preparation of Compounds 43A/43B

Compound 39:

A solution of 26 (812 mg, 2 mmol) and triethylamine (1.12 mL, 8 mmol) indichloromethane (20 mL) was cooled to −78° C. Phosgene (15% in toluene,1.45 mL, 2.2 mmol) was added dropwise and the reaction stirred for 30minutes, then at room temperature for 30 minutes. A solution of2-fluoro-5-methylaniline (677 μL, 6 mmol) in dichloromethane (10 mL) wasadded dropwise and the reaction stirred overnight. The solvent wasremoved by rotary evaporator and the crude co-evaporated withdiethylether (50 mL). Product was precipitated from diethylether andfiltered, then suspended in saturated aqueous NaHCO₃ and filtered. Theproduct was dried under high vacuum to yield 1.05 g (1.88 mmol, 94%) of39 as light brown solid.

Compound 40:

Compound 39 (500 mg, 0.9 mmol) was dissolved in 4:1 MeOH/THF (125 mL)and loaded into a Parr vessel. Pd(OH)₂ (200 mg, 40% weight) was addedand the reaction agitated under 50 psi of H₂. Reaction was stopped after90 minutes and the slurry filtered through CELITE. Filtrate wasevaporated, then co-evaporated with dichloromethane (50 mL). Product wasprecipitated from 10:1 hexane/dichloromethane and filtered. Significantdechlorination was observed. Procedure was repeated with another batchof X (534 mg, 0.96 mmol) and less Pd(OH)₂ (105 mg, 20% weight).Dechlorination was still observed. Precipitates were combined and driedunder high vacuum to yield 745 mg (1.6 mmol, Y=86%) of 40A/40B as lightbrown solid (65:35 chlorinated/dechlorinated).

Compound 41:

40 (643 mg, 1.38 mmol) and ethyl 4-bromobutyrate (491 mg, 2.5 mmol) weredissolved in dry N,N-dimethylformamide (12 mL). K₂CO₃ (380 mg, 2.75mmol) was added and the reaction stirred at 45° C. overnight. Solventwas removed by rotary evaporator and the residue co-evaporated withdichloromethane (50 mL). Product was precipitated from water, filtered,and dried under high vacuum to yield 587 mg (1.01 mmol, Y=73%) 41A/41Bas brown powder.

Compound 42:

NaOH pellets (400 mg, 10 mmol) were dissolved in 1:1 THF/H₂O (10 mL). 41(1.13 g, 2 mmol) was added and the reaction stirred for 4 hours. Solventwas removed by rotary evaporator and the resulting crust suspended inH₂O, Solution was acidified to pH 1 using concentrated HCl. Slurry wasfiltered to yield sticky hygroscopic solid. Solid was frozen in −80° C.freezer to yield 472 mg (0.85 mmol, 43%) of 42A/42B as dark brownpowder, which was used in the next reaction without furtherpurification.

Compound 43:

2-Oxa-7-azaspiro[3.5]nonane hemioxalate (221 mg, 1.01 mmol) was stirredin water (3 mL) with Amberjet 4200 (3 g, 12 mmol). After 90 minutes, theslurry was filtered and the filtrate lyophilized to yield the free baseas white foam. Free base, 42A/42B (373 mg, 0.68 mmol), andN,N-dimethylpyridin-4-amine (83 mg, 0.68 mmol) were dissolved in dryN,N-dimethylformamide (10 mL).N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (169 mg,0.88 mmol) was added and the reaction stirred overnight. Solvent wasremoved by rotary evaporator and the product precipitated from saturatedaqueous NaHCO₃. Slurry was filtered and washed with hexane to yield avery sticky gum, which was dried under high vacuum to yield 379 mg (0.57mmol, 84%) chocolate brown powder (3:1 chlorinated/dechlorinated).Purification and separation of final products was achieved by prep LC.

Isolated 78 mg (0.12 mmol) of 43A as white solid. m/z 663.3 [M]. ¹H-NMR(CDCl₃, 400 MHz): δ 1.85 (4H, m); 2.28 (2H, m); 2.35 (3H, s); 3.42 (2H,t); 3.54 (2H, t); 4.02 (3H, s); 4.25 (2H, t); 4.45 (4H, q); 6.48 (1H,d); 6.86 (1H, m); 6.99 (1H, dd); 7.08 (1H, s); 7.13 (1H, dd); 7.21 (1H,d); 7.31 (1H, s); 7.43 (1H, s); 7.50 (1H, s); 7.89 (1H, m); 8.30 (1H,d); 8.49 (1H, d). Isolated 19 mg (0.03 mmol) of 43B as white solid. m/z629.3 [M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 1.85 (4H, dt); 2.28 (5H, m);2.58 (2H, t); 3.41 (2H, t); 3.53 (2H, t); 4.00 (3H, s); 4.21 (2H, m);4.44 (4H, q); 6.34 (1H, d); 6.74 (1H, m); 6.86 (1H, t); 6.99 (2H, d);7.44 (1H, s); 7.51 (3H, m); 7.91 (1H, d); 8.42 (1H, d).

Example 16 Preparation of Compound 48

Compound 44

To a solution of 3-oxetanol (21.0 g, 283.80 mmol) and3-(phenylmethoxy)-1-propanol (65 g, 283.80 mmol) in anhydrousN,N-dimethylformamide (200 mL) was added NaI (8.51 g, 56.76 mmol) andNaH (29.3 g, 709.50 mmol, 60% in mineral oil). The resulting suspensionwas stirred at room temperature overnight. The reaction mixture wascooled to 0° C. and quenched with water (200 mL), followed by 6 N HCl(200 mL). The mixture was extracted with ethyl acetate (300 mL×2) andthe combined organic phases were concentrated in vacuo to afford thecrude product as a brown oil. The crude product was purified by silicacolumn (petroleum ether:ethyl acetate=25:1 to 10:1) to give 30 g(yield=47.6%) of 44 as a colorless oil.

Compound 45

To a solution of 44 (30.0 g, 135.14 mmol) in ethanol (400 mL) was addedPd/C (3.0 g), then this mixture was stirred at room temperature under H₂(1 atm) for 48 h. The reaction mixture was filtered through a pad ofCELITE to remove the solid. The filtrate was concentrated under reducedpressure to give 16 g (yield=89.7%) of 45 as a colorless oil.

Compound 46

To a solution of 45 (30.0 g, 142.45 mmol), Compound 126 of Example 9(22.56 g, 170.94 mmol) and triphenyl phosphine (74.64 g, 284.90 mmol) indry tetrahydrofuran (800 mL) was added diisopropyl azodicarboxylate(57.55 g, 284.90 mmol) in dry tetrahydrofuran (100 mL) dropwise at 0° C.After addition, the temperature of the reaction mixture was increased toroom temperature and stirred for 3 h. The reaction mixture wasconcentrated in vacuo to give a residue. The residue was diluted withethyl acetate (1.0 L) and washed with water (500 mL×2). The organicphase was concentrated to give crude product as a brown residue. Thecrude product was purified by silica column (petroleum ether:ethylacetate=5:1 to 1:1) to give 48.9 g (yield=105.7%) of 46 as light yellowsolid (this product contained triphenylphosphine oxide and was useddirectly in the next step without further purification).

Compound 47

A mixture of 46 (48.90 g, 150.55 mmol), 7 (13.55 g 75.28 mmol) andCs₂CO₃ (49.05 g, 150.55 mmol) in tetrahydrofuran (500 mL) was stirred at50° C. overnight. The reaction mixture was diluted with ethyl acetate(500 mL) and washed with water (500 mL×2) and brine (500 mL)successively. The organic layer was dried with Na₂SO₄ and concentratedto dryness. The residue was purified by silica column(dichloromethane:methanol=50:2) to give 25.2 g (yield=38.8%) of 47 as abrown solid.

Compound 48

A mixture of 47 (9 g, 20.84 mmol) and 10 (9 g crude) in toluene (100 mL)was stirred at 70° C. for 3 h. The reaction mixture was concentrated invacuo and the residue was diluted with dichloromethane (200 mL) andwashed with water (100 mL×2). The organic layer was concentrated and theresidue was purified by silica column (dichoromethane:methanol=50:1 to10:1) to give 6 g of solid. The solid was washed with toluene (20 mL) togive 5.1 g (yield=42%) of 48 as an off-white solid. m/z 583.3 [M+H]⁺.¹H-NMR (CDCl₃, 400 MHz): δ 2.18 (2H, m); 2.30 (3H, s); 3.59 (2H, t);4.04 (3H, s); 4.30 (2H, t); 4.59 (3H, m); 4.79 (2H, t); 6.77 (1H, m);6.88 (1H, m); 7.18 (1H, dd); 7.26 (1H, s); 7.35 (1H, s); 7.52 (1H, s);7.60 (2H, d); 7.93 (1H, d); 8.31 (1H, d); 8.63 (1H, s).

Example 17 Preparation of Compound 49

A mixture of 47 (2.40 g, 5.56 mmol) and 7 (2.40 g crude) indichloromethane (30 mL) was stirred at room temperature for 5 h. Thereaction mixture was diluted with dichloromethane (200 mL) and washedwith water (100 mL). The organic layer was concentrated and the residuewas purified by silica column (dichloromethane:methanol=100:1 to 10:1)to give 1.15 g (yield=37.2%) of 49 as a pink solid. m/z 556.3 [M+H]⁺.¹H-NMR (CDCl₃, 400 MHz): δ 2.19 (2H, m); 2.43 (3H, s); 3.59 (2H, t);4.04 (3H, s); 4.31 (2H, t); 4.58 (3H, m); 4.79 (2H, m); 5.99 (1H, s);7.19 (1H, dd); 7.26 (2H, d); 7.51 (1H, s); 8.42 (1H, d); 8.64 (1H, s).

Example 18 Preparation of Compound 50

Compound 50

A solution of diisopropyl azodicarboxylate (174 mg, 0.86 mmol) was addedto a solution of compound 40A of Example 15 (230 mg, 0.50 mmol),2-(oxetan-3-yloxy)ethanol (112 mg, 0.85 mmol) prepared in accordancewith the process for 45 in Example 16, and triphenyl phosphine (224 mg,0.85 mmol) in dry N,N-dimethylformamide (3 mL) at 0° C. After addition,the temperature of the reaction mixture was increased to roomtemperature and stirred for 8 h. The solvent was evaporated and theresidue was partitioned between sodium bicarbonate and dichloromethanewith 10% methanol. The organic solution was separated and dried withmagnesium sulfate. The solvent was evaporated. The residue was dissolvedin dichloromethane and applied on a pad of silica. The pad was elutedwith dichloromethane, ethyl acetate, ethyl acetate with 5% methanol andethyl acetate with 10% methanol. The fractions containing product(Rf=0.5 in ethyl acetate with 10% methanol) were combined and evaporatedleaving a yellow oil. Final purification was achieved by prep LC.Isolated 36 mg (0.07 mmol, yield=13%) of 50 as white solid. m/z 583.2[M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 2.21 (2H, m); 2.35 (3H, s); 3.60 (2H,t); 4.02 (3H, s); 4.32 (2H, t); 4.61 (3H, m); 4.77 (2H, t); 6.50 (1H,d); 6.88 (2H, m); 7.00 (1H, dd); 7.15 (2H, m); 7.25 (1H, d); 7.47 (1H,s); 7.50 (1H, s); 7.86 (1H, d); 8.30 (1H, d); 8.51 (1H, d).

Example 19 Preparation of Compound 52

Compound 51

A solution of 4-chloro-6,7-dimethoxyquinazoline (7.23 g, 30 mmol) in dryN,N-dimethylformamide (72 mL) was sparged with N₂ during the sequentialaddition of NaH (3.6 g of 60% dispersion in mineral oil, 90 mmol),potassium carbonate (12.42 g, 90 mmol), and 4-amino-3-chlorophenol-HCl(8 g, 44 mmol). Reaction was heated to 100° C. and stirred for 2 hours.Solution was cooled to room temperature and the solvent evaporated byrotary evaporator. Remaining residue was co-evaporated withdichloromethane (50 mL) and the remaining crust suspended in water,sonicated, and filtered. Product was dried under high vacuum to give5.88 g (17.76 mmol, yield=59%) purple powder 51, which was used in thenext reaction without further purification.

Compound 52

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. 2-(Morpholin-4-ylmethyl)aniline (175 mg, 0.91 mmol) wasadded and the reaction stirred overnight. Solvent was evaporated byrotary evaporator, then co-evaporated with diethyl ether (20 mL). Crudesolid was precipitated from diethyl ether and purified by reverse phaseflash chromatography to yield 86 mg (0.16 mmol, yield=52%) of 52 as palepink solid. m/z 550.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ (4H, s); 3.54(2H, s); 3.58 (4H, s); 3.98 (6H, d); 7.01 (1H, t); 7.25 (2H, t); 7.32(1H, dd); 7.40 (1H, s); 7.56 (1H, s); 7.58 (1H, d); 7.88 (1H, d); 7.97(1H, d); 8.58 (1H, s); 8.75 (1H, s); 9.09 (1H, s).

Example 20 Preparation of Compound 53

Compound 53

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. 4-(Morpholin-4-ylmethyl)aniline (175 mg, 0.91 mmol) wasadded and the reaction stirred overnight. Solvent was evaporated byrotary evaporator, then co-evaporated with diethyl ether (20 mL). Crudesolid was precipitated from diethyl ether and purified by reverse phaseflash chromatography to yield 25 mg (0.05 mmol, yield=15%) of 53 as palepink solid. m/z 550.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ (4H, s); 3.40(2H, s); 3.57 (4H, s); 3.98 (6H, d); 7.23 (2H, d); 7.29 (1H, dd); 7.40(1H, s); 7.43 (2H, d); 7.55 (1H, m); 8.22 (1H, d); 8.36 (1H, s); 8.57(1H, s); 9.40 (1H, s).

Example 21 Preparation of Compound 54

Compound 54

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. 2-[(4-piperazin-1-yl)methyl]aniline (187 mg, 0.91 mmol) wasadded and the reaction stirred overnight. Solvent was evaporated byrotary evaporator, then co-evaporated with diethyl ether (20 mL). Crudesolid was precipitated from diethyl ether and purified by reverse phaseflash chromatography to yield 52 mg (0.09 mmol, yield=31%) of 54 aslight brown solid. m/z 563.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ 2.50(11H, m); 3.59 (2H, s); 3.98 (6H, d); 7.03 (1H, t); 7.27 (1H, t); 7.31(1H, dd); 7.55 (1H, s); 7.58 (1H, d); 7.86 (1H, d); 8.00 (1H, d); 8.58(1H, s); 8.80 (1H, s); 9.03 (1H, s).

Example 22 Preparation of Compound 55

Compound 55

Triethylamine (505 μL, 3.63 mmol) was added to a solution of 51 (300 mg,0.91 mmol) in dichloromethane (30 mL) and cooled to −78° C. Phosgene(661 μL of 15% solution in toluene, 1.00 mmol) was added dropwise andthe reaction stirred for 30 minutes at −78° C., then at room temperaturefor 30 minutes. 4[(4-piperazin-1-yl)methyl]aniline (557 mg, 2.72 mmol)was added and the reaction stirred overnight. Solvent was evaporated byrotary evaporator, then co-evaporated with diethyl ether (20 mL). Crudesolid was precipitated from diethyl ether, then dissolved in 10%methanol/dichloromethane. Organics were washed with saturated aqueoussodium bicarbonate, dried over MgSO₄, and filtered. Solvent wasevaporated by rotary evaporator and the product dried under high vacuumto give 311 mg (0.55 mmol, yield=61%) of 55 as a tan solid. m/z 563.2[M+H]⁺. ¹H-NMR (CDCl₃, 400 MHz): δ 2.30 (3H, s); 2.48 (8H, bs); 3.49(2H, t); 4.07 (6H, d); 6.79 (1H, s); 7.13 (1H, s); 7.20 (1H, dd); 7.31(1H, d); 7.33 (1H, s); 7.34 (3H, s); 7.52 (1H, s); 8.35 (1H, d); 8.63(1H, s).

Example 23 Preparation of Compound 56

Compound 56

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. A dichloromethane solution of4-(3-dimethylamino-propoxy)-phenylamine dihydrochloride (243 mg, 0.91mmol) and triethylamine (254 μL, 1.82 mmol) was added and the reactionstirred overnight. Solvent was evaporated by rotary evaporator, thenco-evaporated with diethyl ether (20 mL). Crude solid was precipitatedfrom diethyl ether and purified by reverse phase flash chromatography toyield 39 mg (0.07 mmol, yield=24%) of 56 as tan solid. m/z 552.2 [M].¹H-NMR (DMSO-d6, 400 MHz): δ 1.88 (2H, m); 2.27 (6H, s); 3.98 (8H, m);6.89 (2H, d); 7.29 (1H, dd); 7.38 (3H, m); 8.22 (1H, d); 8.31 (1H, s);8.57 (1H, s); 9.28 (1H, s).

Example 24 Preparation of Compound 57

Compound 57

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. A dichloromethane solution of2-[(3-aminobenzyl)(methyl)amino]ethanol dihydrochloride (230 mg, 0.91mmol) and triethylamine (254 μL, 1.82 mmol) was added and the reactionstirred overnight. Solvent was evaporated by rotary evaporator, thenco-evaporated with diethyl ether (20 mL). Crude solid was precipitatedfrom diethyl ether and purified by reverse phase flash chromatography toyield 84 mg (0.16 mmol, yield=52%) of 57 as light brown solid. m/z 538.2[M]. ¹H-NMR (DMSO-d6, 500 MHz): δ 3.57 (4H, s); 3.96 (8H, m); 6.98 (1H,m); 7.29 (2H, m); 7.40 (2H, m); 7.56 (2H, s); 8.22 (1H, d); 8.39 (1H,s); 8.58 (1H, s); 9.50 (1H, s)

Example 25 Preparation of Compound 58

Compound 58

Triethylamine (168 μL, 1.21 mmol) was added to a solution of 51 (100 mg,0.3 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (218μL of 15% solution in toluene, 0.33 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. 5-Chloro-2-(4-ethylpiperazin-1-yl)aniline (218 mg, 0.91mmol) was added and the reaction stirred overnight. Solvent wasevaporated by rotary evaporator, then co-evaporated with diethyl amine(20 mL). Crude solid was precipitated from diethyl amine and purified byreverse phase flash chromatography to yield 22 mg (0.04 mmol, yield=12%)of 58 as light brown solid. m/z 597.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ1.04 (3H, t); 2.42 (2H, d); 2.53 (2H, s); 2.61 (3H, s); 2.82 (4H, s);3.98 (6H, d); 7.03 (1H, d); 7.17 (1H, d); 7.32 (1H, d); 7.40 (1H, s);7.57 (1H, d); 8.00 (1H, dd); 8.58 (1H, s); 9.24 (1H, s).

Example 26 Preparation of Compound 59

Compound 59

Triethylamine (335 μL, 2.4 mmol) was added to a solution of 51 (200 mg,0.6 mmol) in dichloromethane (10 mL) and cooled to −78° C. Phosgene (436μL of 15% solution in toluene, 0.66 mmol) was added dropwise and thereaction stirred for 30 minutes at −78° C., then at room temperature for30 minutes. N2,N2-dimethylquinoline-2,6-diamine (339 mg, 1.8 mmol) wasadded and the reaction stirred overnight. Solvent was evaporated byrotary evaporator, then co-evaporated with diethyl ether (20 mL). Crudesolid was precipitated from diethyl ether and purified by reverse phaseflash chromatography to yield 82 mg (0.15 mmol, yield=25%) of 59 as darkgreen solid. m/z 545.2 [M]. ¹H-NMR (DMSO-d6, 500 MHz): δ 3.14 (6H, s);3.98 (6H, d); 7.06 (1H, d); 7.31 (1H, d); 7.40 (1H, s); 7.54 (3H, d);7.91 (1H, s); 7.96 (1H, d); 8.25 (1H, d); 8.58 (1H, s).

Example 27 VEGFR2Binding Assay

A competition binding assay (DISCOVERX KINOMESCAN™) was used to measurethe ability of a compound to compete for binding of an immobilizedadenosine triphosphosphate (ATP) site directed ligand using a DNA-taggedvascular endothelial growth receptor 2 (VEGFR2) as the target. Theability of the test compound to compete with the immobilized ligand wasmeasured using quantitative polymerase chain reaction (qPCR) of the DNAtag (Fabian, M. A. et al., 23 Nature Biotechnology 329-336 (2005);Karaman, M. W. et al., 26 Nature Biotechnology 127-132 (2008)).

A VEGFR2 tagged T7 phage strain was prepared in an Escherichia coli (E.coli) derived from the BL21 strain. The E. coli were grown to log-phase,infected with VEGFR2 tagged T7 phage and then incubated with shaking at32° C. until lysis. The lysate containing the kinase was thencentrifuged and filtered to remove cell debris. Affinity resin for theVEGFR2 assay was prepared by treating Streptavidin-coated magnetic beadswith a biotinylated small molecule ligand for 30 minutes at roomtemperature. The beads were blocked with excess biotin and then washedwith blocking buffer (SEABLOCK (PIERCE), 1% bovine serum albumin, 0.17%phosphate buffered saline, 0.05% TWEEN 20, 6 mM dithiothreitol). Thebinding reaction was initiated by combining in a well of a polystyrene96-well plate, DNA tagged VEGFR2, liganded affinity beads and the serialdiluted test compound in 1× binding buffer (20% SEABLOCK, 0.17×phosphate buffered saline, 0.05% TWEEN 20, 6 mM dithiothreitol) in afinal volume of 0.135 ml. The assay plates were incubated at roomtemperature with shaking for 1 hour and then the beads were washed withwash buffer (1× phosphate buffered saline, 0.05% TWEEN 20). The beadswere re-suspended in elution buffer (1× phosphate buffered saline, 0.05%TWEEN 20, 0.05 μM non-biotinylated affinity ligand) and incubated atroom temperature with shaking for 30 minutes. The VEGFR2 concentrationin the eluate was measured using qPCR.

An 11-point dose response curve of 3-fold serial diluted test compoundstarting at 1 μM was used to determine the VEGFR2 binding constant(K_(d)). The compounds were prepared in 100% DMSO at 100× the final testconcentration and the diluted to 1× in the assay for final DMSOconcentration of 1%. Binding constants were calculated with standarddose-response curve using the Hill equation with Hill slope set to −1.Curves were fit using a non-linear least square fit with theLevenberg-Marquardt algorithm.

TABLE 3 K_(d) values of selected compounds. Compound ID Kd  9 0.49 123.2 14 37 15 20 16 0.52 17 1 21 58 25 4.8 30 0.69 35 1.3 38 10 43a 3143b 8.7 48 14 49 0.98 50 25 52 120 53 3.3 54 27 55 1.7 56 2.4 57 1.3 5810

Example 28 Novel Compounds Prepared as Mucus Penetrating Particles (MPP)

A number of the compounds of the present invention synthesized inaccordance with the preceding Examples were formulated as mucuspenetrating particles (MPP). Specifically, Compounds 9, 25, 12, 49, 48,35, 38, 55, 15, and 16 were each milled in the presence of PLURONIC F127(F127) to determine whether F127 1) aids particle size reduction toseveral hundreds of nanometers and 2) physically (non-covalently) coatsthe surface of generated nanoparticles with a mucoinert coating thatwould minimize particle interactions with mucus constituents and preventmucus adhesion.

A milling procedure was employed in which an aqueous dispersioncontaining coarse drug particles and PLURONIC F127 (F127) was milledwith grinding medium until particle size was reduced below 400 nm asmeasured by dynamic light scattering. Table 4 lists the size ofparticles and polydispersity index (a measure of the width of theparticle size distribution) generated using this technique. In thisexample suspensions were buffered using DPBS (Dulbecco'sPhosphate-Buffered Saline) which yields a suspension that is bothisotonic and has a physiologically relevant pH.

TABLE 4 Particle size for compounds formulated as MPP Compound ParticlePolydispersity ID Size (nm) Index (PDI)  9 241 0.179 25 203 0.164 12 3130.165 49 222 0.133 48 167 0.166 35 189 0.223 38 242 0.211 55 190 0.31415 137 0.247 16 225 0.197

In order to determine whether the generated nanoparticles have reducedinteractions with mucins and are therefore able to move within mucuswithout becoming trapped, particles were incubated with humancervicovaginal mucus (CVM) and observed via dark field microscopy. In atypical experiment, ≦1 μL of the nanoparticle suspension was added to 20μl of CVM. Observations were made in a minimum of three distinct andrandomly selected areas of the CVM sample. Control particles with knownbehavior were used to qualify the CVM sample as appropriate for theassay. For all compounds (except compound 55) listed in Table 4,mobility in mucus was observed and therefore the nanoparticles weredeemed to be effective MPP. Compound 55 is soluble in the low pH of CVM,which is only an issue in the assay, not in intended target sites, suchas the eye, which has a neutral pH.

Example 29 Back of the Eye Drug Exposure from Topical Installation ofNovel Compound MPP

Pharmacokinetic (PK) studies of Compounds 9, 25, and 12 formulated asMPP in accordance with Example 28 were performed in order to demonstratethat topical installation of MPP formulations of these compounds resultsin drug exposure at the back of the eye. The typical study design isshown in Table 5. Dutch-belted rabbits were used in these studies.

TABLE 5 Study design for PK evaluation of a novel compound MPP Number ofTerminal Animals Time- Test (n/time Dose Frequency/ points Group Articlepoint) Volume Duration (hours) 1 MPP, 0.5% 4 50 μL BID 5 days 0.5 2 MPP,0.5% 4 50 μL BID 5 days 1 3 MPP, 0.5% 4 50 μL BID 5 days 2 4 MPP, 0.5% 450 μL BID 5 days 4 5 MPP, 0.5% 6 50 μL BID 5 days 8 6 MPP, 0.5% 6 50 μLBID 5 days 12 BID = twice a day

The resulting drug exposure in the back of the eye is shown in Table 6.

TABLE 6 C_(max) and AUC_(0-last) drug concentrations for compoundstested in PK C_(max) C_(max) AUC_(0-last) AUC_(0-last) Compound RetinaChoroid Retina Choroid ID (nM) (nM) (nM*h) (nM*h)  9 110  693 915 540025 33 574 297 5790 12 39 265 308 2450

The portion of the retina and choroid collected and analyzed was an 8 mmround punch where the macula is located in humans. These resultsdemonstrate that topical installation of novel compound MPP result indrug exposure in the retina and choroid in vivo. Furthermore theseresults demonstrate the design of the molecule itself affects drugexposure as varying levels of exposure were measured for the differentcompounds tested.

Draize-Ocular Irritation assessments were also performed during thesestudies and no irritation was seen for any of the formulations.

EQUIVALENTS AND SCOPE

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process.

Furthermore, the invention encompasses all variations, combinations, andpermutations in which one or more limitations, elements, clauses, anddescriptive terms from one or more of the listed claims is introducedinto another claim. For example, any claim that is dependent on anotherclaim can be modified to include one or more limitations found in anyother claim that is dependent on the same base claim. Where elements arepresented as lists, e.g., in Markush group format, each subgroup of theelements is also disclosed, and any element(s) can be removed from thegroup. It should it be understood that, in general, where the invention,or aspects of the invention, is/are referred to as comprising particularelements and/or features, certain embodiments of the invention oraspects of the invention consist, or consist essentially of, suchelements and/or features. For purposes of simplicity, those embodimentshave not been specifically set forth in haec verba herein. It is alsonoted that the terms “comprising” and “containing” are intended to beopen and permits the inclusion of additional elements or steps. Whereranges are given, endpoints are included. Furthermore, unless otherwiseindicated or otherwise evident from the context and understanding of oneof ordinary skill in the art, values that are expressed as ranges canassume any specific value or sub-range within the stated ranges indifferent embodiments of the invention, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,but rather is as set forth in the appended claims. Those of ordinaryskill in the art will appreciate that various changes and modificationsto this description may be made without departing from the spirit orscope of the present invention, as defined in the following claims.

1. A compound of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein: R₁ is hydrogenor optionally substituted C₁₋₆ alkyl; R₂ is heterocyclyl; X is a bond,—O—, or —C(═O)—; each instance of R₃ is independently selected from thegroup consisting of hydrogen, F, Cl, Br, I, CN, and OH; Y is CH or N; Zis optionally substituted aliphatic, optionally substitutedheterocyclylalkyl, optionally substituted aryl, optionally substitutedheteroaryl, or optionally substituted quinolyl; m is independently 0, 1,2, 3, or 4; and n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.2. The compound of claim 1, wherein the compound is of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein: each instance ofR₄ is independently hydrogen, optionally substituted C₁₋₆ alkyl, F, Cl,Br, I, or CN; and j is 0, 1, or
 2. 3. The compound of claim 1, whereinthe compound is of Formula (II-a):

or a pharmaceutically acceptable salt thereof.
 4. The compound of claim1, wherein the compound is of Formula (II-b):

or a pharmaceutically acceptable salt thereof.
 5. The compound of claim1, wherein the compound is of Formula (II-c):

or a pharmaceutically acceptable salt thereof.
 6. The compound of claim1, wherein the compound is of Formula (II-c1):

or a pharmaceutically acceptable salt thereof.
 7. The compound of claim1, wherein the compound is of Formula (II-c2):

or a pharmaceutically acceptable salt thereof.
 8. The compound of claim1, wherein the compound is of Formula (II-c3):

or a pharmaceutically acceptable salt thereof.
 9. The compound of claim1, wherein the compound is of Formula (II-c4):

or a pharmaceutically acceptable salt thereof.
 10. The compound of claim1, wherein the compound is of Formula (III):

or a pharmaceutically acceptable salt thereof, wherein: each instance ofR₅ is independently hydrogen, optionally substituted C₁₋₆ alkyl, F, Cl,Br, I, or CN; and k is 0, 1, 2, 3, 4, or
 5. 11. The compound of claim 1,wherein the compound is of Formula (III-a):

or a pharmaceutically acceptable salt thereof.
 12. The compound of claim1, wherein the compound is of Formula (III-b):

or a pharmaceutically acceptable salt thereof.
 13. The compound of claim1, wherein the compound is of Formula (III-c):

or a pharmaceutically acceptable salt thereof.
 14. The compound of claim1, wherein the compound is of Formula (III-c1):

or a pharmaceutically acceptable salt thereof.
 15. The compound of claim1, wherein the compound is of Formula (III-c2):

or a pharmaceutically acceptable salt thereof.
 16. The compound of claim1, wherein the compound is of Formula (III-c3):

or a pharmaceutically acceptable salt thereof.
 17. The compound of claim1, wherein the compound is of Formula (III-c4):

or a pharmaceutically acceptable salt thereof.
 18. The compound of claim1, wherein the compound is of Formula (IV):

or a pharmaceutically acceptable salt thereof, wherein Z₁ is branched orunbranched, acyclic or cyclic C₁₋₆ alkyl.
 19. The compound of claim 1,wherein the compound is of Formula (IV-a):

or a pharmaceutically acceptable salt thereof.
 20. The compound of claim1, wherein the compound is of Formula (IV-a1):

or a pharmaceutically acceptable salt thereof.
 21. The compound of claim1, wherein the compound is of Formula (IV-a1-i):

or a pharmaceutically acceptable salt thereof.
 22. The compound of claim1, wherein the compound is of Formula (IV-a1-ii):

or a pharmaceutically acceptable salt thereof.
 23. The compound of claim1, wherein the compound is of Formula (IV-a1-iii):

or a pharmaceutically acceptable salt thereof.
 24. The compound of claim1, wherein the compound is of Formula (IV-a1-iv):

or a pharmaceutically acceptable salt thereof.
 25. The compound of claim1, wherein the compound is of Formula (IV-b):

or a pharmaceutically acceptable salt thereof.
 26. The compound of claim1, wherein the compound is of Formula (IV-b1):

or a pharmaceutically acceptable salt thereof.
 27. The compound of claim1, wherein the compound is of Formula (IV-b1-i):

or a pharmaceutically acceptable salt thereof.
 28. The compound of claim1, wherein the compound is of Formula (IV-b1-ii):

or a pharmaceutically acceptable salt thereof.
 29. The compound of claim1, wherein the compound is of Formula (IV-b1-iii):

or a pharmaceutically acceptable salt thereof.
 30. The compound of claim1, wherein the compound is of Formula (IV-b1-iv):

or a pharmaceutically acceptable salt thereof.
 31. The compound of claim1, wherein the compound is of Formula (V):

or a pharmaceutically acceptable salt thereof, wherein each of e and fis independently 1, 2, or
 3. 32. The compound of claim 1, wherein thecompound is of Formula (V-a):

or a pharmaceutically acceptable salt thereof.
 33. The compound of claim1, wherein the compound is of Formula (V-a1):

or a pharmaceutically acceptable salt thereof.
 34. The compound of claim1, wherein the compound is of Formula (V-a1-i):

or a pharmaceutically acceptable salt thereof.
 35. The compound of claim1, wherein the compound is of Formula (V-a1-ii):

or a pharmaceutically acceptable salt thereof.
 36. The compound of claim1, wherein the compound is of Formula (V-a1-ii):

or a pharmaceutically acceptable salt thereof.
 37. The compound of claim1, wherein the compound is of Formula (V-a1-iv):

or a pharmaceutically acceptable salt thereof.
 38. The compound of claim1, wherein the compound is of Formula (V-b):

or a pharmaceutically acceptable salt thereof.
 39. The compound of claim1, wherein the compound is of Formula (V-b1):

or a pharmaceutically acceptable salt thereof.
 40. The compound of claim1, wherein the compound is of Formula (V-b1-i):

or a pharmaceutically acceptable salt thereof.
 41. The compound of claim1, wherein the compound is of Formula (V-b1-ii):

or a pharmaceutically acceptable salt thereof.
 42. The compound of claim1, wherein the compound is of Formula (V-b1-iii):

or a pharmaceutically acceptable salt thereof.
 43. The compound of claim1, wherein the compound is of Formula (V-b1-iv):

or a pharmaceutically acceptable salt thereof.
 44. The compound of claim1, wherein R₂ is of the formula:

wherein each instance of p and q is independently 0, 1, 2, 3, or
 4. 45.The compound of claim 44, wherein R₂ is of the formula:


46. The compound of claim 1, wherein R₂ is of the formula:

wherein each instance of p, q, s, and t is independently 0, 1, 2, 3, or4.
 47. The compound of claim 46, wherein R₂ is of the formula:


48. The compound of claim 1 of one of the following formulae:


49. A pharmaceutical composition comprising a compound of claim 1, or apharmaceutically acceptable salt thereof, and a pharmaceuticallyacceptable carrier.
 50. The pharmaceutical composition of claim 49,wherein the pharmaceutical composition is suitable for delivery to theeye. 51.-64. (canceled)
 65. A compound of Formula (VI):

or a pharmaceutically acceptable salt thereof, wherein: R₁ is hydrogenor optionally substituted C₁₋₆ alkyl; R₂ is heterocyclyl; X is a bond,—O—, or —C(═O)—; each instance of R₃ is independently selected from thegroup consisting of hydrogen, F, Cl, Br, I, CN, and OH; Y is CH or N; Zis optionally substituted aliphatic, optionally substitutedheterocyclylalkyl, optionally substituted aryl, optionally substitutedheteroaryl, or optionally substituted quinolyl; m is independently 0, 1,2, 3, or 4; and n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.